The Secret of the Superseding Tax Return
It is one of the few ways to undo a married filing joint tax return
In the tax world, there is rarely an opportunity for a do-over; however, if a taxpayer files a tax return and later wants to undo something on it, the taxpayer can generally file a superseding return to do so.
A taxpayer’s right to file a superseding return is rooted in long-standing Supreme Court precedent. In Chief Counsel Advice 202026002, the IRS said that Haggar Co. v. Helvering, 308 U.S. 389 (1940) has “come to stand for the proposition that a superseding return, whether filed on extension or not, is effective for most purposes.”
As the March 15 and April 15 deadlines for tax year 2025 quickly approach, it is critical to understand why and how a taxpayer should consider filing a superseding return.
What is a Superseding Return?
Internal Revenue Manual 21.6.7.4.10(2) (10-01-2025) states:
An amended (Form 1040-X) or corrected (duplicate) return filed on or before the due date or the extended due date is a superseding return…
The Taxpayer Advocate explains how a superseding return is different from an amended return:
Generally, superseding returns are intended to replace or supersede (hence the name) a timely filed original return with a subsequent timely filed return… The changes made by a superseding return are, in effect, incorporated into and relate back to the original return…
In contrast, an amended return changes items reported on an original return but is filed after the original filing deadline, including extensions… The filing of an amended return modifies the original filed return, and the IRS treats it as the taxpayer’s return of record.
The IRS is not legally required to process an amended return. As the Supreme Court stated in Badaracco v. Comm., 464 U.S. 386 (1984):
…the Internal Revenue Code does not explicitly provide either for a taxpayer's filing, or for the Commissioner's acceptance, of an amended return; instead, an amended return is a creature of administrative origin and grace.
Reasons to File a Superseding Return
The primary reason to file a superseding return rather than an amended return is to change an irrevocable election; certain elections made on an original return cannot be changed on an amended return. Two common examples include:
A joint return election under §6013, and
An election to credit a refund to the following year’s estimated tax payments under Treas. Reg. §301.6402-3.
Important note: Internal Revenue Manual 21.6.7.4.10(4) (10-01-2025) states that a taxpayer filing a superseding return to change an irrevocable election must file it before the unextended due date.
Therefore, a taxpayer who timely filed a married filing jointly tax return can file a superseding return before the unextended Form 1040 deadline and change to a married filing separately tax return, which negates joint and several liability.
Another reason to file a superseding return versus an amended return is to reduce the §6694 or §6695 estimated tax penalties if the superseding return shows a lower total tax. For example, under Rev. Rul. 83-36, if an individual taxpayer files a superseding return, the revised tax amount is used to determine whether the total prepayments meet the 90% of current-year tax prong. If the taxpayer files an amended return, the tax shown on the original return is used to calculate the 90% prong.
Partnerships that cannot opt out of the centralized partnership audit regime (CPAR) can file a superseding return by the extended due date (if an extension was filed) and avoid the administrative adjustment request (AAR) process.
A superseding return can generally be used to correct erroneous tax items in the same way as an amended return; however, there may be no material benefit to the superseding return other than providing the correct information as soon as possible to the IRS, potentially avoiding future IRS inquiries.
How to File a Superseding Return
To electronically file a superseding return, whether it is Form 1040 for individuals, Form 1065 for partnerships, or Form 1120 for corporations, the entire return should be prepared and electronically transmitted with the “superseding return” box checked in the software; there is no box on the actual form to indicate a superseding return. The IRS has a website that explains this for corporate returns.
If the return must be mailed to the IRS, write “SUPERSEDING RETURN - IRM 21.6.7.4.10” at the top of the first page to facilitate proper processing. The statement is not a formal procedural requirement, but could avoid it being flagged as a duplicate return. In addition, be sure the IRS receives the return before the applicable due date.
It is a best practice to file automatic extensions for partnership and corporate tax returns, even if not needed, to preserve the right to file a superseding return.
The decision for Form 1040 extensions is more complicated because Treas. Reg. §1.6081-4(b)(4) requires a proper estimate of the tax liability for the extension to be valid, which requires significantly more effort. In addition, a Form 1040 extension extends by six months one of the time periods that must run for a tax to be discharged in a bankruptcy proceeding; an unnecessary extension could cause certain tax debts not to be discharged. My prior article on best practices for Form 1040 extensions contains a lot more information on these issues.