Letter 31C: Duplicate returns filed; explanation requested

What Letter 31C is

Sent by Accounts Management when two returns have posted for the same year and the assistor cannot tell from the returns and a phone attempt whether the second is a true duplicate, an additional (supplemental) return or an amendment (IRM 21.7.9.4.1.4(3), Oct. 1, 2026). The distinction decides the arithmetic: "A tax increase on a supplemental return is increased for the amount reported on the supplemental return. A tax increase on an amended return is increased for the difference between the original and amended returns" (IRM 21.7.9.4.1.4). Meanwhile a -A freeze holds any refund or offset on the year.

The deadline

40-day suspense (IRM 21.7.9.4.1.4(3)).

What to do

Answer in writing with both returns marked: which figures are correct, whether the second return replaces or adds to the first, and whether any payment sent with it was for the year's tax. If the second return was meant as a correction, say so and attach a Form 945-X for the difference. If it was a true duplicate, say so and ask for the -A freeze to be released.

Duplicate, supplemental or amended

When two Form 945s (or 941s) arrive for the same year, the IRS has to decide what the second one is, and the three possibilities produce three different results. A true duplicate is the same return filed twice, usually because a payroll provider and the client both filed, or a paper copy followed an electronic one; it should be discarded. A supplemental return reports additional tax not on the first, and the account is increased by the full amount on it. An amended return restates the year, and the account is increased or decreased by the difference between it and the original. Since 2009 the correct way to amend is Form 945-X, so a second plain Form 945 is ambiguous by construction, and the IRS tries the return itself and a phone call before giving up. Letter 31C is the written request that follows, and while it is open a freeze holds any refund or offset on the year.

Answering it within the 40 days

Reply in writing with copies of both returns, marked up. State which figures are correct, whether the second return replaces the first or adds to it, and whether any payment that accompanied it was tax for the year or something else. If the second return was meant as a correction, say so and attach a Form 945-X for the difference, because that is the instrument the IRS wants and it ends the ambiguity; include a Form 945-A if the liability by date changed. If it was a true duplicate, say so plainly and ask that the freeze be released. If it was supplemental (you found additional withholding after filing), say so and address the deposit penalty that will follow on the late-deposited amount. Send it by a method that proves the date; after 40 days with no reply the IRS decides from the returns alone, which usually means treating the second as supplemental and assessing the full amount again. The duplicate and superseding returns page covers how the campus handles each case, and the Form 945-X page covers the correction itself.

Questions about Letter 31C

Have a different notice? The IRS notice decoder lists all 77 in the order they tend to arrive.