Form 5564 (Notice of Deficiency – Waiver): the four paths and what each one gives up

What Form 5564 Is

Form 5564, Notice of Deficiency – Waiver, comes with a CP3219A, the notice of deficiency the IRS often sends after a CP2000 the taxpayer did not resolve. The IRS page "Understanding your CP3219A notice" says the notice "isn't a bill or audit" and tells a taxpayer who agrees with the change to "Reply to us with the enclosed Form 5564." A deficiency is the extra tax the IRS says you owe. Assessment is the IRS recording that tax as owed on your account, which lets it send a bill and collect. A signed Form 5564 is a waiver under IRC §6213(d).

The amount on the form can differ from the earlier notice. The IRS page says the amounts on Form 5564 "may not match your prior notice amount due" because "you can't challenge all items in U.S. Tax Court." The figures on the form itself show what a signature covers.

If a Letter 3219 or Letter 531 came with a waiver form, IRC §6213(d) governs it too, and the same petition deadline applies. The reply steps quoted below come from the IRS page for the CP3219A; follow the reply instructions printed on your own letter.

The Four Paths and What Each One Gives Up

Every path runs against one deadline: the last day to petition the Tax Court, 90 days after the mailing date, or 150 days if the IRS addressed the notice to a person outside the United States (IRC §6213(a)). The notice of deficiency clock computes it. The choice among the paths belongs to the taxpayer and the practitioner. This page sets out what the law and the IRS say each one does.

Agree and sign. Signing lifts the bar in IRC §6213(a) on assessing and collecting the amount you waive, so you consent to its assessment (IRC §6213(d)). The IRS can then assess that amount and send a bill without waiting for the 90 or 150 days to end, and once it assesses under the waiver, you cannot withdraw it (26 CFR §301.6213-1(d)). Signing files no petition. For the items you stop disputing, the court route after assessment runs through payment: pay, file a refund claim (IRC §7422(a)), then sue in a federal district court or the Court of Federal Claims (28 U.S.C. §1346(a)(1)).

Reply with a signed statement and documents. The IRS page tells a taxpayer with more information to "reply to us with Form 5564 and provide any documentation along with a signed statement explaining which items you disagree with and the reason." The signed statement explains the disagreement; the IRS page does not ask you to sign the waiver to make this reply. This reply asks the IRS to reconsider and files nothing with the Tax Court. The IRS page says its work with you during the 90 days "won't extend the time you have to file a petition in Tax Court."

Petition the Tax Court. A petition you file by the last day lets a judge decide the dispute before you pay, and IRC §6213(a) bars assessment and levy until the decision becomes final, apart from rare jeopardy and termination cases (IRC §6851, §6852, §6861). The Tax Court charges a $60 filing fee, which it can waive, and offers a small tax case procedure for income tax disputes of up to $50,000 for any one taxable year (IRC §7463(a)). One cost is specific to the petition: IRC §6214(a) lets the Court find a deficiency larger than the notice states if the IRS asserts the claim at or before the hearing. Interest runs on every path: the Tax Court guidance and the IRS page both say interest runs on any unpaid tax until you pay it in full.

Do nothing. The IRS page states the result: "If we don't hear from you and you don't file a petition, we'll assess the proposed changes and send you a bill." After that, the court route runs through payment: pay the tax, file a refund claim (IRC §7422(a)), and then sue in a federal district court or the Court of Federal Claims (28 U.S.C. §1346(a)(1)).

Agreeing to Part of the Deficiency

IRC §6213(d) lets a taxpayer waive the assessment restrictions for "the whole or any part of the deficiency." So the paths can split by item: a taxpayer can waive the part they accept and petition on the part they dispute, as long as the petition reaches the Tax Court by the last day. The waived part then follows the first path, and the disputed part follows the third.

Identity Theft and Amended Returns

If someone used your name and Social Security number to earn the income on the notice, the IRS page says to send your reply with a completed Form 14039, Identity Theft Affidavit.

If the CP3219A is correct and you have other income, credits or expenses to report, the IRS page points to an amended return on Form 1040-X, which you send with Form 5564.

A tax professional who contacts the IRS for you needs a Form 2848, Power of Attorney and Declaration of Representative, which the IRS page names for that purpose. A practitioner files a Tax Court petition for you only if the Tax Court has admitted that practitioner to practice before it.

Where to Go Next

The notice of deficiency clock computes the last day. The notice pages explain each letter: CP3219A, Letter 3219 and Letter 531. The appeal channel router covers audit reconsideration after assessment, and the CSED calculator computes how long the IRS has to collect once it assesses.

Common Questions