Qualified Amended Returns: How to Avoid Tax Penalties

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Jason B. Freeman

Jason B. Freeman

Managing Member


Mr. Freeman is the founding member of Freeman Law, PLLC. He is a dual-credentialed attorney-CPA, author, law professor, and trial attorney.

Mr. Freeman has been named by Chambers & Partners as among the leading tax and litigation attorneys in the United States and to U.S. News and World Report’s Best Lawyers in America list. He is a former recipient of the American Bar Association’s “On the Rise – Top 40 Young Lawyers” in America award. Mr. Freeman was named the “Leading Tax Controversy Litigation Attorney of the Year” for the State of Texas for 2019 and 2020 by AI.

Mr. Freeman has been recognized multiple times by D Magazine, a D Magazine Partner service, as one of the Best Lawyers in Dallas, and as a Super Lawyer by Super Lawyers, a Thomson Reuters service. He has previously been recognized by Super Lawyers as a Top 100 Up-And-Coming Attorney in Texas.

Mr. Freeman currently serves as the chairman of the Texas Society of CPAs (TXCPA). He is a former chairman of the Dallas Society of CPAs (TXCPA-Dallas). Mr. Freeman also served multiple terms as the President of the North Texas chapter of the American Academy of Attorney-CPAs. He has been previously recognized as the Young CPA of the Year in the State of Texas (an award given to only one CPA in the state of Texas under 40).

A “qualified amended return” is an amended tax return that, if properly filed before a taxpayer is “on the IRS’s radar,” protects a taxpayer against accuracy-related penalties—in layman’s terms, it is a get-out-of-jail-free card.  The Treasury regulations, in effect, provide a “safe harbor” that allows a taxpayer to avoid tax penalties.  A qualified amended return must, by definition, be filed before the IRS begins an investigation of the taxpayer or the promoter of a transaction in which the taxpayer participated.  Much like the IRS’s voluntary disclosure practice and streamlined filing compliance procedure, the qualified-amended-return provisions are intended to encourage voluntary compliance by giving taxpayers an avenue to proactively fix past mistakes.

A Qualified Amended Return Must Be Timely

A “qualified amended return” is an amended return that is filed after the due date of the original return and before the earliest of several important events.  In other words, the amended return must be “timely.”

Specifically, a taxpayer can file a qualified amended return (or administrative adjustment under section 6227) if the original tax return was not fraudulent and the amended return is filed before:

The date that the IRS contacts a promoter, organizer or material advisor concerning a listed transaction for which the taxpayer has claimed a tax benefit.

What Penalties Can Be Avoided Through a Qualified Amended Return?

A qualified amended return allows a taxpayer to avoid accuracy-related penalties that would otherwise be imposed on an “understatement” of tax that is reflected on the taxpayer’s original tax return.

Generally, section 6662 imposes an accuracy-related penalty on an underpayment of tax.  The section 6662 penalty applies to understatements attributable to any of the following items:

  1. Negligence or disregard of rules or regulations.
  2. Any substantial understatement of income tax.
  3. Any substantial valuation misstatement under chapter 1.
  4. Any substantial overstatement of pension liabilities.
  5. Any substantial estate or gift tax valuation understatement.
  6. Any disallowance of claimed tax benefits by reason of a transaction lacking economic substance (within the meaning of section 7701(o)) or failing to meet the requirements of any similar rule of law.
  7. Any undisclosed foreign financial asset understatement.
  8. Any inconsistent estate basis.
  9. Any overstatement of the deduction provided in section 170(p).

Accuracy-related penalties under section 6662 can range from 20% to 40%.

A Qualified Amended Return Does Not Avoid Fraud Penalties

Notably, a qualified amended return does not protect against fraud penalties.  That is, where an understatement relates to a fraudulent position on the taxpayer’s original return, a qualified amended return will not insulate the taxpayer from fraud penalties.  A taxpayer with a fraudulent tax return may, however, be a candidate for a voluntary disclosure.

What is a John Doe Summons?

The regulations provide that an amended return will not constitute a qualified amended return if the IRS has already served a John Doe summons on a third party with respect to the taxpayer’s tax liability.  A John Doe summons is a summons that does not identify the person with respect to whose liability the summons is issued.  See Release the Kraken?—In re Tax Liability of John Does.  Since Congress codified the IRS’s power to issue John Doe summonses in 1976, courts have increasingly approved the IRS’s use of John Doe summonses.  See Coinbase: The Government Strikes Back, AgainSee also IRS Gets Green Light to Seek Information from Third Parties Regarding Panama Offshore Legal Services.

What is a Listed Transaction?

For taxpayers who have claimed tax benefits from undisclosed listed transactions, an amended return will not be treated as a qualified amended return unless it is filed before the IRS contacts a promoter, organizer, seller, or material advisor concerning the listed transaction.   A listed transaction is defined as a transaction that is the same as or substantially similar to one of the types of transactions that the IRS has determined to be a tax avoidance transaction and identified by notice, regulation, or another form of published guidance as a listed transaction. Tax Shelter Penalties: Listed Transactions and Reportable Transactions.

An undisclosed listed transaction, therefore, is a transaction that: (1) is the same or substantially similar to a listed transaction as defined in Section 1.6011-4(b)(2); and (2) was not previously disclosed by the taxpayer.

A taxpayer is no longer eligible to file a qualified amended return once: (1) the IRS first contacts them regarding an examination of their liability under section 6707(a) with respect to the undisclosed listed transaction; or (2) the IRS issues a request for information relating to the listed transaction.

Notably, under Treasury regulations, a qualified amended return includes an amended return that is filed solely to disclose information pursuant to Section 1.6011-4, provided that the taxpayer also makes the required disclosure to the Office of Tax Shelter Analysis.


A qualified amended return can be a formidable defense against IRS accuracy-related penalties.  A qualified amended return, however, must be filed “timely”—that is, before the taxpayer or the issue is already on the IRS’s radar.  Once the IRS begins an examination or criminal investigation, it is too late.  But for some taxpayers, a qualified amended return can serve as a veritable a get-out-of-jail-free card when it comes to civil penalties.


Expert Penalty Defense Attorneys

Need assistance with IRS penalty defense? Each individual civil penalty has different penalty defenses. It is important to raise the proper penalty defenses with the IRS at the appropriate time. Freeman Law can help you navigate these complex issues. We handle all types of cases including civil, failure-to-file and failure-to-pay, accuracy-related, fraud, tax shelters, international tax, employment tax, and trust fund recovery penalties. Schedule a consultation or call (214) 984-3000 to discuss your tax concerns.