Taxed on a Retirement Withdrawal? How To Fight a 1099-R Bill
The IRS taxed a 401(k) or IRA distribution at the full amount and added a 10% penalty. Here's how to fight a 1099-R deficiency in Tax Court.
The IRS says you owe tax on a retirement distribution—maybe one you barely remember taking, maybe one you rolled over, maybe one you reported but the IRS taxed at the full amount anyway. On top of the income tax, there's often a 10% "additional tax" for taking the money early. A CP2000 didn't fix it. Now you have a Notice of Deficiency and 90 days to file in Tax Court.
This is a substantive merits guide, not a procedural one. A retirement distribution dispute is really three separate fights, and they have different answers:
- Is the distribution even taxable—and how much of it? Basis, rollovers, and Roth rules can shrink or erase the taxable amount.
- Does the 10% early-distribution additional tax under IRC § 72(t) apply? There is a long list of exceptions, and the payer's form often doesn't reflect the one that fits you.
- Did you miss a required minimum distribution (RMD)? That triggers a separate excise tax under IRC § 4974—now far smaller than it used to be, and waivable.
Winning the first fight often shrinks the second automatically. Let's take them in order, after a quick look at how a single form lands you here.
How a 1099-R Becomes a Deficiency
A Form 1099-R is a third-party information return your plan or IRA custodian files for any distribution of $10 or more. Two patterns put a retirement distribution in front of the Tax Court.
You didn't report it at all. The IRS Automated Underreporter (AUR) program matches the 1099-R against your return, finds nothing, and issues a CP2000 proposing to tax the full "gross distribution"—often plus the § 72(t) 10%. See how to respond to a CP2000 notice for the procedure; this guide is about the merits.
You reported it, but the IRS taxed more than it should have. Most commonly the IRS taxes the gross amount and ignores your basis (after-tax money you already paid tax on), or treats a rollover as a taxable distribution because the form's distribution code didn't capture it.
When the CP2000 doesn't resolve—you disagreed, the IRS rejected your explanation, or you missed the response window—the next step is a Statutory Notice of Deficiency, the 90-day letter. Under IRC § 6213 you have 90 days (domestic) or 150 days (international) to petition the Tax Court before the tax is assessed. See how the 90-day clock protects you and how to file your Tax Court petition.
Who has to prove what. The default rule is that the IRS's determination is presumed correct and you bear the burden of showing it's wrong (Tax Court Rule 142(a); Welch v. Helvering, 290 U.S. 111 (1933)). But because a 1099-R is a third-party information return, IRC § 6201(d) applies the same way it does to any 1099: if you raise a reasonable dispute and have cooperated, the IRS must come forward with reasonable and probative information beyond the form itself. The full burden-of-proof toolkit—§ 6201(d), the predicate-evidence rule, § 7491—is built out in unreported income disputes in Tax Court. Raise § 6201(d) by name; don't re-litigate the whole framework here.
Read Your 1099-R First
Before you argue with a number, understand the form that generated it. Four boxes do the work.
- Box 1 — Gross distribution. The total paid out. The IRS often taxes this whole number.
- Box 2a — Taxable amount. What the payer believes is taxable. For an IRA, the payer usually has no idea about your basis, so box 2a frequently just equals box 1—a guess, not a determination.
- Box 2b — two checkboxes. "Taxable amount not determined" means the payer did not compute the taxable portion and you have to. For nearly all traditional-IRA distributions this box is checked—the payer is telling you box 2a is not authoritative. "Total distribution" just means the account was fully paid out.
- Box 7 — Distribution code(s). The payer's characterization of the distribution. The common ones:
| Code | Meaning |
|---|---|
| 1 | Early distribution, no known exception |
| 2 | Early distribution, exception applies (e.g., SEPP, age-55 separation, IRS levy) |
| 3 | Disability |
| 4 | Death |
| 7 | Normal distribution (age 59½ or older) |
| G | Direct (trustee-to-trustee) rollover—not taxable |
| J | Early Roth distribution, no known exception |
| T | Roth distribution, exception applies |
| Q | Qualified Roth distribution (tax-free) |
Here is the key point most people miss: code "1" does not mean no exception exists. It means the payer wasn't told one applied. And box 2a does not bind you when box 2b is checked. These two settings—code "1" and box 2a equal to box 1—generate most of these deficiencies, and both are routinely wrong for the taxpayer. Form 5329 is how you override code "1." Basis on Form 8606 is how you override box 2a.
Fight 1: Is the Distribution Even Taxable, and How Much?
The income-tax fight comes first, because basis, rollovers, and Roth rules each carve into the taxable amount—and whatever falls out of income here also falls out of the § 72(t) base in Fight 2.
Basis—Your After-Tax Money Comes Back Tax-Free
IRC § 72(a) pulls distributions into gross income, and IRC § 408(d)(1) does the same for IRAs. But the taxable amount is not automatically the gross amount. The portion of a distribution that returns your after-tax basis—your "investment in the contract"—is not taxable. "Investment in the contract" is the total of premiums or contributions you paid with money that was already taxed, minus amounts you've already taken back tax-free. Sections 72(b) and 72(c) set the mechanics for annuitized streams; § 72(e) governs lump sums.
Where does basis come from?
- Nondeductible traditional-IRA contributions, tracked on Form 8606 (Nondeductible IRAs). Form 8606 is your running ledger of after-tax dollars. It figures how much of each distribution is a tax-free return of basis versus taxable earnings or pre-tax money. The IRS's CP2000 almost never accounts for Form 8606 basis—it taxes the box 1 gross. This is one of the most winnable issues in the whole area.
- After-tax 401(k) contributions and designated Roth (Roth 401(k)) money.
One trap to know about. The pro-rata rule in § 408(d)(2) treats all your traditional, SEP, and SIMPLE IRAs as a single contract, all distributions in a year as one distribution, and measures value at year-end. So basis is recovered ratably across all your IRAs—you cannot point to one account and call the whole withdrawal "just my nondeductible money." A taxpayer who thinks "I'm only taking out my after-tax contributions" is wrong if they hold other pre-tax IRA money. The taxable amount comes out as a blend.
The practical move: if box 2b "taxable amount not determined" is checked and you have basis, you compute the taxable amount on Form 8606, and the deficiency falls to the extent of that basis.
Rollovers—A Distribution You Rolled Over Isn't Taxable
Even if box 7 says code "1," a distribution you actually rolled over within the rules is not taxable. There are two parallel regimes:
- Employer plans — § 402(c). An "eligible rollover distribution" moved into an eligible retirement plan within 60 days is excluded from income. Some things can't be rolled over because they aren't eligible rollover distributions: required minimum distributions, substantially-equal-periodic-payment streams, and hardship distributions.
- IRAs — § 408(d)(3). Same 60-day rule.
Three rollover sub-issues come up again and again.
1. The 60-day rule and the self-certification waiver. Miss the 60 days and the distribution is taxable—unless the IRS waives the deadline. Section 408(d)(3)(I) authorizes a waiver where enforcing the 60 days "would be against equity or good conscience, including casualty, disaster, or other events beyond the reasonable control of the individual." Rev. Proc. 2020-46 lets a taxpayer self-certify eligibility for that waiver using a model letter, for an enumerated list of reasons—financial-institution error, a check that was misplaced and never cashed, serious illness, a death in the family, and others. The IRS's Verifying rollover contributions to plans page explains how a receiving plan can accept a self-certified late rollover. If you blew the 60 days for a reason on the list, this can rescue the whole distribution.
2. The once-per-year IRA-to-IRA limit. Under § 408(d)(3)(B), you may make only one nontaxable 60-day IRA-to-IRA rollover in any one-year (365-day) period, and that limit is aggregated across all of your IRAs—not counted per account. This is the Bobrow rule (more below). Critically, trustee-to-trustee transfers and direct rollovers do not count against this limit and are unlimited—money that never came into your hands was never a "distribution" at all. So if the IRS treats a direct transfer as a taxable distribution, your first response is that it was trustee-to-trustee and never a § 408(d)(3) distribution to begin with.
3. Plan-loan offsets. When a 401(k) loan is "offset"—the unpaid balance netted against your account—because you left the job or the plan terminated, § 402(c)(3)(C) gives you an extended rollover deadline: until the due date (including extensions) of your tax return for that year, not the usual 60 days. Don't confuse this with a § 72(p) deemed distribution (below), which cannot be rolled over at all.
Roth Distributions—Qualified vs. Non-Qualified
Roth IRA distributions follow their own rules under § 408A(d), and the IRS's CP2000 frequently ignores them.
- A qualified distribution is entirely tax-free. It must be made after the 5-taxable-year period (starting with the first year you made any Roth contribution) and meet one of: you're 59½ or older; it's paid to a beneficiary after death; it's attributable to disability; or it's a qualified first-time-homebuyer distribution (up to $10,000).
- For a non-qualified distribution, the ordering rules in § 408A(d)(4) decide what comes out: your contributions come out first (always tax- and penalty-free, because you already paid tax on them), then conversions, then earnings last. So a taxpayer who withdrew no more than the total they'd contributed owes nothing—even if box 7 codes it as an early Roth distribution (code J). The IRS's automated match doesn't apply the ordering rules; you do.
- The 5-year rule runs separately for contributions versus conversions. The detail lives in IRS Pub. 590-B—if your case turns on it, work from that.
Plan Loans and Deemed Distributions
A loan from an employer plan that exceeds the § 72(p) limits (generally the lesser of $50,000 or half your vested balance) or fails the repayment terms (level payments at least quarterly over no more than five years) is treated as a taxable deemed distribution—and a deemed distribution cannot be rolled over. Keep this separate from the plan-loan offset above, which can be rolled over. (Distributions from non-qualified annuities carry their own parallel 10% additional tax under § 72(q), with its own exceptions—but most readers here won't encounter it.)
Fight 2: The § 72(t) 10% Additional Tax on Early Distributions
If you took the money before age 59½, the IRS almost certainly added a 10% "additional tax" under § 72(t). This is the second fight, and it's distinct from the income tax.
What It Is—and What It Isn't
Section 72(t)(1) increases your tax by "10 percent of the portion of such amount which is includible in gross income." Two things follow from that wording.
First, the 10% applies only to the includible portion. So basis and rolled-over amounts that fell out under Fight 1 also fall out of the § 72(t) base. Winning part of Fight 1 wins part of Fight 2 automatically.
Second—and this is the sharpest doctrinal point in the area—§ 72(t) is an "additional tax," not a penalty. That distinction decides how you can and can't attack it (see below).
The Full Exception List (IRA vs. Plan)
Each exception below knocks out the 10% on the amount it covers. The catch is that several apply only to employer plans, several only to IRAs, and a few to both. This table reproduces the IRS's authoritative chart, Retirement topics — Exceptions to tax on early distributions (last reviewed 11 December 2025), with the Code section the IRS cites:
| Exception | IRC section | Qualified plans (401(k), etc.) | IRAs (incl. SEP/SIMPLE) |
|---|---|---|---|
| Age 59½ | 72(t)(2)(A)(i) | Yes | Yes |
| Death of participant/owner | 72(t)(2)(A)(ii) | Yes | Yes |
| Total and permanent disability | 72(t)(2)(A)(iii) | Yes | Yes |
| Substantially equal periodic payments (SEPP) | 72(t)(2)(A)(iv) | Yes | Yes |
| Separation from service in/after the year you turn 55 (age 50 or 25 years' service for qualified public-safety employees) | 72(t)(2)(A)(v), 72(t)(10) | Yes | No (plan only) |
| IRS levy on the account | 72(t)(2)(A)(vii) | Yes | Yes |
| ESOP dividend pass-through | 72(t)(2)(A)(vi) | Yes | n/a |
| Unreimbursed medical expenses over 7.5% of AGI | 72(t)(2)(B) | Yes | Yes |
| Health-insurance premiums while unemployed (12+ weeks) | 72(t)(2)(D) | No | Yes (IRA only) |
| Qualified higher-education expenses | 72(t)(2)(E) | No | Yes (IRA only) |
| Qualified first-time homebuyer (up to $10,000) | 72(t)(2)(F) | No | Yes (IRA only) |
| Qualified reservist called to active duty | 72(t)(2)(G) | Yes | Yes |
| QDRO payment to an alternate payee | 72(t)(2)(C) | Yes | n/a (plan only) |
| Birth or adoption (up to $5,000) | 72(t)(2)(H) | Yes | Yes |
| Emergency personal expense (one per year, up to $1,000) | 72(t)(2)(I) | Yes | Yes |
| Domestic-abuse victim (lesser of $10,000 or 50% of the account) | 72(t)(2)(K) | Yes | Yes |
| Disaster-recovery distribution (up to $22,000) | 72(t)(2)(M), 72(t)(11) | Yes | Yes |
| Terminally ill (physician-certified) | 401(k)(2)(B)(i)(I) | Yes | n/a (plan only) |
| Corrective/returned excess contributions | 401(k)(8)(D), 402(g)(2)(C); IRA: 408(d)(4) | Yes | Yes |
| Rollovers (in-plan Roth or within 60 days) | 402(c), 408(d)(3), 408A(d)(3) | Yes | Yes |
Two things to watch:
- The age-55 separation exception is plan-only. Roll a 401(k) into an IRA and you lose it. Several of the most useful exceptions—higher education, first-time homebuyer, unemployed health-insurance premiums—run the other way and are IRA-only. Which account the money came from can decide whether an exception is even available.
- SIMPLE IRAs have a 25% trap. A distribution from a SIMPLE IRA within the first two years of participation carries a 25% additional tax, not 10%.
SEPP—Substantially Equal Periodic Payments
If you're under 59½ and need ongoing income, substantially equal periodic payments (SEPP, sometimes called a 72(t) plan) are the escape valve. You take a fixed series of withdrawals computed under one of three IRS methods—required-minimum-distribution, fixed amortization, or fixed annuitization—and the 10% doesn't apply.
For any series beginning on or after 1 January 2023, the governing guidance is Notice 2022-6 (it superseded the older Rev. Rul. 2002-62—don't rely on the older one). The maximum interest rate you can assume is the greater of 5% or 120% of the federal mid-term rate for one of the two months before the first payment.
The danger is busting the plan. Under § 72(t)(4) the series must run unmodified until the later of five years or age 59½. Change it early—other than for death or disability—and you owe not just the 10% on the current year but a recapture tax: all the § 72(t) tax that would have applied in the earlier years, plus interest. SEPP is a commitment, not a one-time fix.
Why You Can't Beat § 72(t) on a Penalty-Approval Argument
In other parts of a deficiency case, a powerful pro se move is to challenge whether the IRS got the written supervisory approval that IRC § 6751(b) requires before assessing a penalty. That argument does not work against the § 72(t) 10%—because § 72(t) is a tax, not a penalty.
The Tax Court settled this in Grajales v. Commissioner, 156 T.C. No. 3 (2021), affirmed by the Second Circuit at 47 F.4th 58 (2022). The court held that "the I.R.C. sec. 72(t) exaction is a 'tax' rather than a 'penalty', 'addition to tax', or 'additional amount' and so is not subject to the written supervisory approval requirement of I.R.C. sec. 6751(b)." Relying on the reported precedent El v. Commissioner, 144 T.C. 140 (2015), the court gave three reasons: the statute itself calls the exaction a "tax"; other Code sections refer to it as a plain "tax"; and it sits in the chapter for normal taxes, not the chapter for penalties and additions to tax. (In Grajales, it was the taxpayer arguing that § 6751(b) should apply, over $90.86 of § 72(t) tax—and the court said no. Grajales and El were both represented, not pro se cases.)
What this means for you:
- You cannot defeat the § 72(t) 10% by arguing the IRS lacked § 6751(b) approval. Don't spend a word on it.
- The § 6662 accuracy-related penalty does not attach to the § 72(t) amount itself—again, because it's a tax, not an underpayment penalty.
- The two ways to actually beat § 72(t) are to fit an exception (Form 5329) or to knock the underlying amount out of income (Fight 1).
A § 6662 penalty can still ride on an underpayment of the ordinary income tax on the distribution—that's a separate animal, covered below.
Form 5329—Claiming the Exception the Payer Didn't Code
When box 7 says code "1" but an exception actually applies, Form 5329 (Additional Taxes on Qualified Plans (Including IRAs) and Other Tax-Favored Accounts) is how you fix it. Part I computes the § 72(t) additional tax and is where you enter the exception code to claim your exception. The IRS says it plainly: if you received a distribution that meets an exception but box 7 doesn't show one, use Form 5329 to indicate the correct exception. That is the move when box 7 is coded "1."
Filing the form is not the same as winning, though—you still have to prove the facts. The disability exception is the cautionary tale. In Trainito v. Commissioner, T.C. Summary Op. 2015-37 (a non-precedential Summary Opinion, useful only as an illustration), a Boston city worker with type-2 diabetes took a retirement distribution on 22 April 2011 and filed Form 5329 claiming the disability exception. He suffered a diabetic coma weeks later, on 12 June. The court denied the exception: under § 72(t)(2)(A)(iii) and § 72(m)(7), the disability must exist at the time of the distribution, and the relevant date was 22 April, not the June hospitalization. Diabetes alone, without proof it prevented "substantial gainful activity" on the distribution date, wasn't enough. The precedential authority for that standard is Dwyer v. Commissioner, 106 T.C. 337 (1996), which found no qualifying disability where a taxpayer sought periodic professional consultation but did not meet the regulation's standard.
The lesson: a disability claim has to be proven as of the distribution date, with contemporaneous medical records and, ideally, treating-physician testimony. If the payer had coded box 7 as "3" (disability), there'd be no fight at all; absent that, Form 5329 plus proof is the path.
Fight 3: Missed RMDs and the § 4974 Excise Tax
If the dispute is about a required minimum distribution you didn't take, this is a separate—and now much cheaper—problem.
The RMD beginning age is 73. Under § 401(a)(9), the applicable age is 73 for someone who reaches 72 after 31 December 2022 (and rises to 75 for those who reach 74 after 31 December 2032). Your required beginning date is April 1 of the year after the later of reaching that age or retiring—though owners of more than 5% of the employer can't use the retirement deferral.
The excise tax shrank dramatically. Miss an RMD and § 4974 imposes an excise tax on the shortfall. SECURE 2.0 cut the rate from 50% to 25%, and down to 10% under § 4974(e) if you correct the shortfall within the correction window—which runs from when the tax is imposed until the earliest of (a) the date a notice of deficiency is mailed, (b) the date the tax is assessed, or (c) the last day of the second tax year after the year the tax was imposed.
There's a reasonable-cause waiver. Under § 4974(d), the IRS may waive the tax entirely if you show the shortfall "was due to reasonable error" and "reasonable steps are being taken to remedy" it. You claim it on Form 5329, Part IX—take the corrective distribution now, then attach a reasonable-cause statement. The word is "may," so it's discretionary, not automatic. The framing is the same one you'd use for any penalty abatement request: what went wrong, why it was reasonable, and what you did to fix it.
The takeaway: a missed RMD is fixable cheaply if you act inside the correction window and attach the Part IX waiver.
How Bad Is It? A Worked Example
Numbers make the stakes concrete. Take a laid-off worker, age 45, who cashes out a $40,000 traditional 401(k). Box 7 is coded "1," and box 2a shows $40,000.
| Item | Amount |
|---|---|
| Ordinary income tax (≈22% marginal rate) | ≈ $8,800 |
| § 72(t) additional tax (10% × $40,000) | $4,000 |
| State income tax (illustrative ≈5%) | ≈ $2,000 |
| Rough total exposure | ≈ $14,800 (about 37%) |
And if 20% mandatory withholding applied, only about $32,000 actually reached the worker—so the bill can exceed what's left. (That withholding isn't lost—it's a credit against the tax on the same return and reduces what you still owe—but on an early cash-out it rarely covers the full income-tax-plus-§ 72(t) bill.) That table is also not the whole exposure: like any deficiency, the unpaid tax accrues interest from the original due date of the return until it's paid, and a § 6662 accuracy penalty can ride on the income-tax piece. A bill for an older distribution year has been growing the whole time. When you size up how bad this is, count tax plus penalty plus interest, not just the table. See how interest works on your IRS tax debt.
Now watch how it falls away:
- If $10,000 was after-tax basis (tracked on Form 8606): the taxable amount drops to $30,000. Both the income tax and the § 72(t) shrink, because § 72(t) applies only to the includible portion. That saves roughly 22% + 10% + state on the $10,000—about $3,700.
- If an exception applies—say the distribution paid unreimbursed medical expenses over 7.5% of AGI, or the worker separated from service in/after the year they turned 55: the $4,000 of § 72(t) disappears entirely, even though the income tax remains.
- If the $40,000 was actually rolled over within 60 days (or self-certified late under Rev. Proc. 2020-46): the entire $40,000 falls out of income—both the income tax and the § 72(t) vanish.
The pattern: the ordinary income tax usually stands, but basis, an exception, or a rollover can erase the § 72(t)—and sometimes the whole inclusion.
How To Check the IRS's Math
Never argue with a number you haven't recomputed. Here's the ordered checklist to verify the IRS's figure and find your issue. You can do all of it yourself.
- Pull the 1099-R, and pull your Wage & Income Transcript to confirm exactly what the IRS has under your SSN (see how to get and read your IRS transcripts). Read box 1 versus box 2a versus box 2b versus box 7.
- If box 2b "taxable amount not determined" is checked, the payer didn't compute the taxable amount—you must. Don't accept box 2a as gospel.
- Pull Form 8606, current and all prior years, to total your nondeductible-IRA basis. Recompute the taxable amount using the § 408(d)(2) pro-rata rule across all your IRAs. For a Roth distribution, apply the § 408A(d)(4) ordering rules—contributions come out first, tax-free.
- Pull account and rollover records—statements, the receiving-account deposit confirmation, the dates—to prove any 60-day rollover, trustee-to-trustee transfer, or plan-loan offset. If you missed the 60 days, evaluate self-certification under Rev. Proc. 2020-46.
- Re-derive the taxable amount and whether the § 72(t) 10% applies. Check the exception table. If an exception applies that box 7 didn't code, file or attach Form 5329, Part I with the exception code. For a disability claim, assemble contemporaneous medical proof as of the distribution date.
- For a missed RMD, take the corrective distribution now and file Form 5329, Part IX with a reasonable-cause statement to seek the reduced rate or a full waiver.
- Put it in writing—in your CP2000 response or your petition—and raise § 6201(d) by name (reasonable dispute plus cooperation) so the IRS has to come forward with more than the bare 1099-R.
A clean, recomputed Form 8606 or Form 5329 of your own is the most persuasive exhibit you can put in front of the IRS or the Tax Court. It turns "I disagree" into a specific, documented number.
Penalties, Burden, and the Once-Per-Year Rollover Trap
The accuracy penalty. A § 6662 accuracy-related penalty can ride on the income-tax underpayment (substantial understatement or negligence)—but, per Grajales and El, not on the § 72(t) amount itself. The reasonable-cause defense lives in § 6664(c): an honest misunderstanding, reasonable reliance on a professional, or an isolated error. The full § 6662 / § 6751(b) treatment is in how to fight the IRS accuracy penalty and unreported income disputes in Tax Court—cross-link rather than repeat.
The Bobrow cautionary tale. The leading case on the once-per-year rollover rule is Bobrow v. Commissioner, T.C. Memo. 2014-21. The petitioner was pro se—but he was himself a tax attorney, so he's no model of the typical unrepresented filer. He took three IRA distributions of about $65,000 each and reported none of them, treating each as a separate tax-free rollover. The court held that § 408(d)(3)(B)'s once-per-year nontaxable-rollover limit applies in the aggregate across all of a taxpayer's IRAs, not per account—so only one distribution could be a tax-free rollover and the rest were taxable income. His wife's repayment on the 61st day blew the 60-day rule with no qualifying waiver, and the § 72(t) 10% was sustained on her early distribution. The court also sustained the § 6662 penalty and rejected reasonable cause—his tax expertise cut against him. (The IRS adopted the aggregate rule going forward, and a footnote in the opinion confirms that trustee-to-trustee transfers are unlimited because they aren't "distributions" at all.)
Burden of proof. The Rule 142(a) default puts it on you; § 6201(d) shifts production to the IRS on the 1099-R once you raise a reasonable dispute and cooperate; and § 72(m)(7) expressly puts the disability burden on the taxpayer.
If the Tax Is Right but You Can't Pay
Sometimes the recompute confirms the IRS is correct—the distribution was fully taxable, no exception fits, and the bill stands. For the archetypal reader here—laid off, cashed out the 401(k) to get by—a correct bill you can't pay is its own crisis. Ignoring the notice is the one move that makes it worse. The balance is collectible tax like any other, and you have options: a monthly installment agreement, currently not collectible status if paying anything would leave you unable to cover basic living expenses, or—if you qualify—an offer in compromise to settle for less than the full amount. The overview is in how to resolve your IRS tax debt. Losing the merits fight is not the end of the road.
Get Help: Low-Income Taxpayer Clinics
The archetypal case here—a hardship 401(k) cash-out after a job loss—is a low-dollar, lower-income dispute, which makes it close to a textbook fit for a Low-Income Taxpayer Clinic. If your income is at or below 250% of the poverty line and the dispute is at or below $50,000, an LITC will handle the Tax Court case for free. Around 89% of petitioners represent themselves, but the win rate is lower than for represented petitioners (about 12% pro se versus about 23% represented in the most recent NTA data), so free representation is worth pursuing. The recompute work—basis on Form 8606, the rollover paper trail, the right § 72(t) exception code—is precisely the kind of technical-but-bounded problem an LITC handles well. See also when to get professional help with your tax dispute.
What To Do Now
If you have a Notice of Deficiency for a retirement distribution and the 90 days clock is running:
- Identify the deadline date on the face of the notice. It cannot be extended.
- Pull your 1099-R, your Wage & Income Transcript, and all your Forms 8606 (current and prior years).
- Recompute the taxable amount—account for basis, rollovers, and (for Roth) the ordering rules—and recompute whether a § 72(t) exception applies.
- File or attach Form 5329 to claim an exception box 7 didn't code, or to request the missed-RMD waiver in Part IX.
- Decide whether to file in Tax Court. A timely petition preserves your prepayment forum; filing is $60, with a waiver available. If your dispute is at or below $50,000 per year, you can elect small-case procedures. See how to file your Tax Court petition.
- Do not file an amended return after a Notice of Deficiency issues. It doesn't stop the 90-day clock or moot the deficiency. The Tax Court petition is the forum for changing the number.
- If you missed the 90-day deadline and the deficiency was assessed, audit reconsideration is the fallback.
- Consider an LITC if you meet the income limits—they handle these cases free.
Resources
Statute:
- IRC § 61 — Gross income defined
- IRC § 72 — Annuities; certain proceeds (incl. § 72(t) early-distribution tax)
- IRC § 401 — Qualified pension and profit-sharing plans (incl. § 401(a)(9) RMDs)
- IRC § 402 — Taxability of beneficiary of employees' trust (rollovers; plan-loan offsets)
- IRC § 408 — Individual retirement accounts (IRA distributions and rollovers)
- IRC § 408A — Roth IRAs (qualified distributions, ordering rules)
- IRC § 4974 — Excise tax on accumulations (missed RMD)
- IRC § 6662 — Accuracy-related penalty
- IRC § 6664 — Reasonable cause and good faith
- IRC § 6751 — Procedural requirements (supervisory approval)
- IRC § 6213 — Deficiency procedures and the Tax Court petition
- Tax Court Rule 142 — Burden of Proof
IRS guidance, forms, and publications:
- Retirement topics — Exceptions to tax on early distributions
- Substantially equal periodic payments (SEPP)
- Topic no. 557 — Additional tax on early distributions from traditional and Roth IRAs
- Topic no. 558 — Additional tax on early distributions from retirement plans other than IRAs
- Verifying rollover contributions to plans (Rev. Proc. 2020-46 self-certification)
- Internal Revenue Bulletin 2020-45 (Rev. Proc. 2020-46)
- About Form 1099-R
- About Form 5329 — Additional Taxes on Qualified Plans (Including IRAs)
- About Form 8606 — Nondeductible IRAs
- Pub. 590-B — Distributions From Individual Retirement Arrangements (IRAs)
Cases cited:
- Grajales v. Commissioner, 156 T.C. No. 3 (2021), aff'd, 47 F.4th 58 (2d Cir. 2022)
- El v. Commissioner, 144 T.C. 140 (2015)
- Dwyer v. Commissioner, 106 T.C. 337 (1996)
- Bobrow v. Commissioner, T.C. Memo. 2014-21
- Trainito v. Commissioner, T.C. Summary Op. 2015-37 — non-precedential Summary Opinion, cited only as an illustration
- Welch v. Helvering, 290 U.S. 111 (1933)
Companion articles on TaxCourtHelp:
- How To Respond to a CP2000 Notice
- You Just Got a 90-Day Letter From the IRS — Here's What It Means
- How IRC § 6213 Protects You While Your Tax Court Case Is Pending
- How To File Your Tax Court Petition
- Unreported Income Disputes in Tax Court
- How To Get and Read Your IRS Transcripts
- How To Fight the IRS Accuracy Penalty
- How To Request IRS Penalty Abatement
- How To Request Audit Reconsideration
- How Interest Works on Your IRS Tax Debt
- How To Resolve Your IRS Tax Debt
- How To Find and Use a Low-Income Taxpayer Clinic
- When To Get Professional Help With Your Tax Dispute
This article is for informational purposes only and does not constitute legal or tax advice. For advice specific to your situation, consult a qualified tax professional or attorney.