Overview

When the IRS adjusts a previously filed return—because of third-party data matches, audit findings, or clerical corrections—it may reduce your tax liability and create an overpayment. Claiming a refund after an IRS adjustment is the process of making that overpayment official and getting the IRS to issue the funds (or reverse an earlier assessment). This article explains the steps, timelines, forms, documentation, common pitfalls, and how to respond if your refund is delayed or reduced.

How the IRS adjustment usually starts

The IRS normally communicates an adjustment by sending a notice or letter that explains what changed and why. Read the notice carefully: it will show the lines the IRS changed, the result of the adjustment, and whether an additional refund is expected or a balance is due (IRS: Understanding Your IRS Notice or Letter: https://www.irs.gov/individuals/understanding-your-irs-notice-or-letter).

Key reasons the IRS adjusts a return include:

  • Mismatched wage or nonemployee compensation information (W-2s, 1099s)
  • Missing or corrected credits and deductions
  • Audit or math error corrections
  • Identity theft or fraud investigations

If the IRS’s adjustment reduces your tax liability, you may be entitled to a refund. But getting that refund often requires action on your part.

Step-by-step: What to do when you get an IRS adjustment notice

  1. Read the notice immediately and note the deadline. Notices commonly give 30–60 days to respond, depending on the issue. (See the IRS notice page above.)
  2. Compare the IRS changes to your original return line-by-line. Determine whether the IRS treated an item incorrectly (for example, omitted a deduction or applied income differently).
  3. Gather supporting documents: original W-2/1099 forms, receipts, bank records, corrected statements, and any correspondence with your employer or payer.
  4. Decide on the correct remedy:
  • If the IRS made a mistake and you agree with their numbers but the IRS owes you money, follow the instructions in the notice for claiming the refund.
  • If you disagree, prepare to either provide the requested documentation or file an amended return (Form 1040-X) or a specific claim form (Form 843 in limited cases).
  1. File promptly. For many refund claims, you must file within the statutory time limits (see next section).
  2. Track your claim using IRS tools and keep copies of everything you send.

Which forms will you use?

  • Form 1040-X, Amended U.S. Individual Income Tax Return, is the standard form to correct a previously filed Form 1040 and to claim refunds stemming from those corrections. The IRS explains when to use Form 1040-X and its time limits (About Form 1040-X: https://www.irs.gov/forms-pubs/about-form-1040-x).
  • Form 843, Claim for Refund and Request for Abatement, is used in narrower situations (for example, certain penalties or excise tax refunds and some interest abatements). It is not a substitute for Form 1040-X in most refund cases (About Form 843: https://www.irs.gov/forms-pubs/about-form-843).
  • In identity-theft cases, you may need to file Form 14039 (Identity Theft Affidavit) and follow identity-theft procedures (IRS Identity Theft information: https://www.irs.gov/identity-theft-faqs).

If the IRS adjusted your return and the notice directs you to file an amended return to claim a refund, see our step-by-step guide on filing an amended return (How to File an Amended Return (Form 1040-X): Step-by-Step Guide: https://finhelp.io/glossary/how-to-file-an-amended-return-form-1040-x-step-by-step-guide/).

Time limits and the statute of limitations

You can generally claim a refund by filing an amended return within the later of these two dates:

  • Three years from the date you filed the original return, or
  • Two years from the date you paid the tax.
    This rule is explained on the Form 1040-X instructions (About Form 1040-X: https://www.irs.gov/forms-pubs/about-form-1040-x). Some special rules extend or shorten those limits, so check the instructions and consult a professional when in doubt.

For more on deadlines and when an amended return is still allowed, see our internal explainer: Time Limits for Filing an Amended Return: When You Can Still Claim a Refund (https://finhelp.io/glossary/time-limits-for-filing-an-amended-return-when-you-can-still-claim-a-refund/).

How long will it take to get the refund?

Processing times vary by case complexity. For amended returns and many post-adjustment refund claims, the IRS frequently cites processing periods that can run several weeks to months. The IRS ‘Where’s My Amended Return?’ tool provides status updates for Form 1040-X filings and notes that processing can take up to 16 weeks in many cases (IRS Where’s My Amended Return?: https://www.irs.gov/filing/wheres-my-amended-return). If your refund is tied to an audit or identity-theft review, expect longer timelines.

You can also learn practical tracking steps from our guide: Tracking an Amended Return: What the IRS Processes and How Long It Takes (https://finhelp.io/glossary/tracking-an-amended-return-what-the-irs-processes-and-how-long-it-takes/).

Why your refund might be reduced or offset

Even if the IRS agrees you overpaid, the refund may be reduced by offsets for:

  • Past-due federal or state taxes
  • Delinquent child support
  • Certain federal non-tax debts (Treasury Offset Program)
    See the U.S. Treasury’s Treasury Offset Program (TOP) for details on offsets (https://www.fiscal.treasury.gov/top/).

If your refund is offset, the IRS or Treasury will send a notice explaining the offset and the agency receiving the funds. Keep that notice—it’s necessary if you need to dispute the offset.

Common mistakes and how to avoid them

  • Missing the statute-of-limitations deadline: always check the 3‑year/2‑year rule before assuming you can still claim a refund.
  • Sending incomplete documentation: attach clear copies and a one-page cover letter summarizing why the refund is due.
  • Filing the wrong form: use Form 1040-X for most taxpayer-initiated refund claims tied to income, credits, or deductions. Use Form 843 only when instructions specifically call for it.
  • Ignoring an offset notice: an offset doesn’t mean the refund was lost without recourse; it means another agency received the funds and you must contact that agency to dispute the debt.

Appealing or disputing an IRS adjustment

If you disagree with the IRS adjustment, you have rights:

  • Provide additional documentation within the timeframe in the notice.
  • Request an appeals conference under the IRS Office of Appeals procedures (see appeals instructions on the notice or the IRS appeals pages).
  • If the adjustment is tied to an audit and you disagree with the final letters, you may file a petition with the U.S. Tax Court (in many cases) or pursue other remedies under IRS guidance.
    Refer to the Taxpayer Bill of Rights and appeals guidance on IRS.gov for procedural details (Taxpayer Bill of Rights: https://www.irs.gov/taxpayer-bill-of-rights).

Documentation checklist (what to include when you submit a claim)

  • Copy of the IRS adjustment notice
  • Copy of your original return and any previously filed amended returns
  • Corrected or original W-2s, 1099s, and third-party statements
  • Receipts, invoices, or proof supporting deductions or credits
  • A short cover letter summarizing the change and the requested refund amount
  • Your contact information and taxpayer identification number

Practical examples (real-world scenarios)

  • Missed credit: You filed a return and later discovered an educational credit was omitted. Filing Form 1040-X with the school’s Form 1098-T and corrected calculations can recover the missed credit.
  • Identity theft: The IRS temporarily suspends refund issuance while it investigates identity-theft claims. Filing Form 14039 and following identity-theft procedures helps resolve these cases, but they often take longer to process.
  • Wage mismatch: The IRS adjusts income when employer-reported wages differ from your return. Providing corrected W-2s and payroll statements typically resolves the discrepancy and results in an adjusted refund.

When to get professional help

If the adjustment involves a large dollar amount, identity theft, business income, multistate issues, or appeals, professional representation can save time and reduce errors. In my 15+ years of practice I’ve found that organized documentation and clear, timely responses are the single biggest factors that speed refunds to clients.

See related FinHelp guides for next steps and specialized instructions:

Final tips

  • Act quickly: deadlines matter and quick responses reduce the chance of lost refunds.
  • Keep paper and electronic backups of every submission.
  • Use certified mail or trackable delivery when sending sensitive documents.
  • Monitor your IRS account and get familiar with the IRS notices—most contain clear instructions for next steps.

Professional disclaimer

This article is informational and does not constitute tax advice. For personalized guidance, consult a qualified tax advisor or attorney.

Authoritative sources and further reading

If you need help preparing documentation, evaluating whether to file an amended return, or appealing an adjustment, consider professional assistance to preserve deadlines and maximize your potential refund.