The IRS assesses the deficiency, and the case moves from a dispute about liability to a dispute about collection.

That is the practical consequence. The liability is not necessarily final in every sense, but the forum that would have decided it without payment is generally gone, and every remaining route is narrower. Most require you to pay first. Some address only collection and not the merits. Some are discretionary. One, equitable tolling, is now available in part of the country and unavailable in the rest, and even where available it is an extraordinary remedy rather than an extension.

What follows is what happens, in order, and what each remaining option actually requires. For an explanation of the notice itself and the rules for computing the petition deadline, see What Is a 90-Day Letter From the IRS?

Step One: Assessment

Under I.R.C. section 6213(a), the IRS generally may not assess a deficiency during the period for filing a Tax Court petition, or while a timely filed case is pending. When that period expires without a petition, the restriction lifts and the IRS assesses under section 6201.

Assessment is followed by notice and demand for payment under I.R.C. section 6303, generally within 60 days. If payment is not made, a federal tax lien arises under section 6321 and relates back to the assessment date under section 6322.

Assessment also starts the collection statute. Under I.R.C. section 6502, the IRS generally has 10 years from assessment to collect, subject to statutory suspensions.

Step Two: Collection, and the Notices That Create New Rights

Two later notices matter, because each opens a hearing right that did not exist before.

When the IRS files a notice of federal tax lien, it must notify the taxpayer, who may request a Collection Due Process hearing under I.R.C. section 6320 within 30 days after the fifth business day following the filing.

Before levying, the IRS must generally provide notice of intent to levy and of the right to a hearing under I.R.C. section 6330, and the taxpayer has 30 days to request one. The request is made on Form 12153.

A Collection Due Process hearing is conducted by the IRS Independent Office of Appeals. The taxpayer may raise collection alternatives, spousal defenses, and challenges to the appropriateness of the collection action, and Appeals must consider whether the action balances efficient collection against intrusiveness. Section 6330(c)(3).

Crucially, the underlying liability may be challenged in a Collection Due Process hearing only if the taxpayer did not receive a statutory notice of deficiency and did not otherwise have an opportunity to dispute the liability. Section 6330(c)(2)(B). A taxpayer who received the notice and simply missed the deadline generally cannot use Collection Due Process to relitigate the merits. This is the single most common misunderstanding about the process.

There is also a jurisdictional limit that has recently become sharper. In Commissioner v. Zuch, 605 U.S. ___ (2025), the Supreme Court held that the Tax Court lacks jurisdiction under section 6330 to resolve disputes between a taxpayer and the IRS when the IRS is no longer pursuing the levy. The Court reasoned that the reviewable determination is the binary decision whether the levy may proceed, so when the levy is abandoned there is nothing left to review. The Court noted that a refund suit remains available. The practical effect is that a taxpayer who is using a Collection Due Process case as a vehicle to litigate an issue can lose the forum if the IRS withdraws the levy.

A Collection Appeals Program request is a faster, more limited alternative addressing specific collection actions. It does not provide Tax Court review and does not reach the underlying liability.

Step Three: The Routes That Reach the Merits

Three exist, and each has real prerequisites.

Pay and sue for refund

This is the principal path. Pay the assessed liability, file a timely administrative refund claim, and if it is disallowed or not acted on, sue in a federal district court or the United States Court of Federal Claims. Section 7422(a) supplies the prerequisite that a claim first be duly filed; jurisdiction comes from 28 U.S.C. section 1346(a)(1) for the district courts and section 1491(a)(1) for the Court of Federal Claims.

The obstacles are specific.

Payment must generally be in full. Flora v. United States, 362 U.S. 145 (1960), holds that a district court refund suit requires full payment of the assessment for the year at issue. For divisible taxes, such as the trust fund recovery penalty under section 6672 or employment taxes, payment of the tax attributable to a single unit, such as one employee for one quarter, may suffice to establish jurisdiction, which is why divisible-tax cases are litigated differently.

The claim must be timely. Under I.R.C. section 6511(a), a refund claim generally must be filed within three years from the date the return was filed or two years from the date the tax was paid, whichever is later. Section 6511(b)(2) then limits the amount recoverable by reference to a lookback period. Both rules must be satisfied.

The claim must state its grounds. Treasury Regulation section 301.6402-2(b)(1) requires the claim to set forth each ground and facts sufficient to apprise the Commissioner of the basis for it. Under the variance doctrine, a ground not fairly presented in the administrative claim generally cannot be litigated later. See United States v. Felt & Tarrant Manufacturing Co., 283 U.S. 269 (1931). This is where refund cases are most often lost before they begin.

The suit must be timely. Under I.R.C. section 6532(a), suit generally must be brought within two years after the notice of claim disallowance is mailed.

Audit reconsideration

The IRS may reconsider an assessment where the taxpayer submits information not previously considered, or where there was an IRS computational or processing error. The procedure is administrative and discretionary. See IRM 4.13. It is most useful where the taxpayer never actually participated in the examination, where a substitute for return was prepared under I.R.C. section 6020(b) without the taxpayer's records, or where genuinely new documentation exists.

It is not an appeal, it creates no right to a hearing, and its denial is not directly reviewable. Collection is ordinarily suspended while a reconsideration request is under consideration, but that suspension is administrative practice rather than a statutory right.

Doubt as to liability offer in compromise

An offer in compromise under I.R.C. section 7122 may be based on doubt as to liability, submitted on Form 656-L. This is a limited path, not a merits forum, and it requires a genuine dispute about whether the liability is owed rather than an inability to pay. An offer based on doubt as to collectibility does not contest the amount; it addresses whether it can be collected.

Equitable Tolling: Where the Law Now Stands

After Boechler, P.C. v. Commissioner, 596 U.S. 199 (2022), which held the Collection Due Process petition deadline in section 6330(d)(1) nonjurisdictional and subject to equitable tolling, taxpayers argued the same analysis applies to the deficiency deadline in section 6213(a).

The Tax Court held otherwise in Hallmark Research Collective v. Commissioner, 159 T.C. 126 (2022), concluding the deficiency deadline is jurisdictional.

Four courts of appeals have since rejected that conclusion and held the deadline nonjurisdictional and subject to equitable tolling. The Third Circuit in Culp v. Commissioner, 75 F.4th 196 (3d Cir. 2023); the Second Circuit in Buller v. Commissioner, 160 F.4th 266 (2d Cir. 2025); the Sixth Circuit in Oquendo v. Commissioner, 148 F.4th 820 (6th Cir. 2025); and the Eighth Circuit in Maniktala v. Commissioner, No. 25-1366 (8th Cir. Aug. 11, 2026). Older decisions in the Seventh, Ninth, and Eleventh Circuits treated the deadline as jurisdictional, and the government continues to defend that position.

A third position now exists. In Kyick Holdings, LLC v. Commissioner, No. 25-1429 (1st Cir. Aug. 17, 2026), the First Circuit held section 6213(a) nonjurisdictional but mandatory and not subject to equitable tolling, applying Enbridge Energy, LP v. Nessel, 146 S. Ct. 1074 (2026), which held that a nonjurisdictional deadline can still be immune from tolling where Congress's contrary intent is evident. The court relied on the adjustments and exceptions Congress wrote into the 90-day period itself.

Three points about what this means.

First, the answer depends on where an appeal from your case would lie. Under Golsen v. Commissioner, 54 T.C. 742 (1970), aff'd, 445 F.2d 985 (10th Cir. 1971), the Tax Court follows a squarely on-point decision of the court of appeals to which the case would be appealable. A taxpayer whose appeal would lie to the Second, Third, Sixth, or Eighth Circuit is in a materially different position from one whose appeal would lie to the First, or to a circuit that still treats the deadline as jurisdictional.

Second, nonjurisdictional does not mean tollable, and tollable does not mean forgiving. Kyick Holdings establishes that a court can find the deadline nonjurisdictional and still refuse to toll it. Where tolling is available at all, it requires diligent pursuit of rights and an extraordinary circumstance that stood in the way. Serious illness during the petition period, or a notice that was never delivered because of an IRS error, may qualify. Not reading the mail, a preparer's oversight, or general confusion generally does not.

Third, this area is unsettled, it is moving quickly, and legislation has been proposed. The state of the law when your deadline passed and the state when your case is decided may not be the same. Anyone in this position should have the current authority checked rather than relying on a general description.

What Does Not Work

A few things are worth stating directly.

Requesting an examination reconsideration does not extend or revive the petition period. Continuing to negotiate with the IRS does not extend it either. An amended return is not a substitute for a refund claim in every context and does not create Tax Court jurisdiction. And a Collection Due Process hearing does not reopen the merits for a taxpayer who received the notice of deficiency, which is the situation of most people who missed the deadline.

What to Do Now

Determine the date the notice was mailed and the date the petition was due, and confirm the notice was actually sent to your last known address under I.R.C. section 6212(b). If it was not, the notice may be invalid, which is a different and better argument than tolling.

Determine whether assessment has occurred and what the collection status is, by obtaining account transcripts for each year.

Determine your appellate circuit, because it may determine whether an equitable tolling argument exists at all.

Determine whether full payment is feasible, because that governs whether the refund route is open.

And preserve the record of why the petition was not filed. If a tolling argument is available, it will be built from contemporaneous evidence of diligence and of the circumstance that prevented filing.

What Is a 90-Day Letter From the IRS? · When Should You Hire a U.S. Tax Court Attorney? · How Do I Appeal an IRS Audit? · What Happens During an IRS Appeals Conference?

A missed petition deadline narrows the available options but does not always end the matter, and the correct next step depends on your appellate circuit, the collection posture, and whether payment is feasible. Chase Counsel handles selected federal tax controversy matters and can assess which routes remain open. Learn more at www.ChaseCounsel.Com/federal-tax-controversy.

This article discusses federal tax procedure generally and is not legal advice for any particular taxpayer. The law governing statutory filing deadlines is unsettled and varies by circuit; current authority should be verified for any specific matter.