You respond to an IRS Notice of Deficiency by reading it carefully, deciding whether you agree with the IRS’s proposed changes, and sending your response before the 90-day deadline printed on the notice. Missing that window means the IRS can assess the additional tax without further input from you, so the clock matters as much as the content of your response. If you just opened a CP3219A or Letter 3219 in the mail, and are wondering “how do I respond to an IRS deficiency notice?” here’s what that means and what to do next.
What Is an IRS Notice of Deficiency?
A Notice of Deficiency, sometimes called a “90-day letter,” is the IRS telling you it plans to increase your tax bill. It usually shows up after an audit, or after the IRS spots a mismatch between your return and information reported by an employer, bank, or other third party, such as an unreported 1099. The notice will show the proposed changes, the additional tax and penalties, and a specific date by which you need to act.
This is a formal, legal notice, not a routine letter. The right response depends on whether the IRS got it right.
What to Do in the First 30 Days
Start by confirming three things: the tax year in question, the deadline date printed on the notice (it runs from that date, not the day you opened the envelope), and whether the notice matches the return you actually filed.
From there:
- Pull a copy of the tax return the notice refers to.
- Request an IRS tax transcript if you’re not sure what the IRS is comparing your return against.
- Compare the proposed changes line by line against your own records.
Acting early matters more than usual right now. The IRS has lost roughly 31% of its revenue agent workforce since 2025, according to Yale’s Budget Lab, and staffing gaps like that tend to slow down how quickly the IRS can process responses or answer questions, so build in extra time for any back-and-forth.
Decide Whether You Agree or Disagree
Once you understand the proposed changes, you have two paths. If the IRS is right, agreeing is usually faster and simpler. If you believe the numbers are wrong or missing information, disagreeing preserves your right to have a court review the issue before you owe anything.
If You Agree: Signing Form 5564
If the proposed changes are accurate, sign and return Form 5564, the Notice of Deficiency Waiver, which is typically included with the notice. This tells the IRS you accept the changes so it can assess the tax without waiting out the full 90 days. If you can’t pay the balance in full once it’s assessed, you can also set up a payment plan with the IRS rather than paying it all at once. Keep a copy of the signed form and proof of mailing for your records.
If You Disagree: Filing a Tax Court Petition
If you disagree, you generally need to file a petition with the U.S. Tax Court within 90 days of the notice date (150 days if the notice was mailed to an address outside the country). Filing a petition lets you dispute the deficiency without paying the disputed amount first.
Filing an amended return, Form 1040-X, does not pause or extend that 90-day deadline. If you have new information that supports your position, gather it, but still file the petition to protect your right to be heard in Tax Court.
Documents and Forms You May Need
- The Notice of Deficiency itself (CP3219A or Letter 3219)
- Form 5564, if you agree with the changes
- A Tax Court petition, if you disagree
- A copy of the original return for the year in question
- Supporting records: 1099s, W-2s, receipts, bank statements
- Form 1040-X, if you’re amending based on new information
Your 90-Day Deadline at a Glance
- Day 0: Notice date printed on the CP3219A or Letter 3219
- Day 1–30: Confirm the tax year, request a transcript, compare figures
- Day 31–60: Decide whether to agree or disagree, gather supporting documents
- Day 61–90: Sign and mail Form 5564, or file your Tax Court petition
- After Day 90: The IRS can assess the deficiency if no response was filed
When to Bring in a CPA
A Notice of Deficiency carries real deadlines and real dollar amounts, and it’s easier to get the decision right with a second set of eyes. This is exactly the kind of high-stakes IRS matter that calls for licensed tax resolution services, not a general tax preparer or a volume tax prep shop. Shaun Glenn, CPA, MSA, MST, has spent 15+ years working through IRS notices, audits, and tax controversy matters for churches, nonprofits, schools, and closely held businesses, and can review your notice against your actual filing to help you see where the IRS’s numbers came from.
Before you sign anything or let a deadline pass, it’s worth having someone with CPA-level credentials and a Master of Taxation confirm whether the proposed changes hold up, and whether disagreeing is worth pursuing given your specific facts. If the tax ends up assessed and you can’t pay it, a CPA can also walk you through options like currently not collectible status.
If you’ve received one of these notices and aren’t sure which path fits your situation, Simplicity Financial can help you review the notice and outline your options before the deadline passes. If you’d like to talk through your notice before the deadline, you can contact our trusted CPA in California, Shaun Glenn.
Your Next 90 Days, Simplified
A Notice of Deficiency can look intimidating, but it comes down to two questions: is the IRS right, and do you have 90 days left to act on it? Answer those, gather your documents, and you’ll know whether you’re signing a form or filing a petition. Either way, having a CPA check your notice against your actual return before you respond helps you avoid a decision you can’t undo once the deadline passes.
If you’ve received one of these notices and aren’t sure which path fits your situation, our CPA in California can help you review the notice and outline your options before the deadline passes. Schedule a phone call with Shaun Glenn, CPA, MSA, MST, or schedule a Zoom meeting if you’d rather share the notice on screen.
FAQs About IRS Deficiency Notices
Why did I receive a CP3219A or Letter 3219?
Most often, the IRS spotted a difference between what you reported and what a third party, like an employer or bank, reported to them. It can also follow an audit where the IRS proposed changes you didn’t agree to in writing.
What is a Notice of Deficiency exactly?
It’s the IRS telling you it plans to charge you more tax unless you respond. It’s a formal notice with legal weight, not a routine reminder, and it starts a 90-day countdown.
What happens if I don’t respond at all?
The IRS can assess the additional tax once the 90 days pass, without further input from you. Not responding is treated the same as agreeing.
Can I dispute a deficiency notice without paying first?
Yes. Filing a petition with the U.S. Tax Court within the 90-day window lets you dispute the amount before you owe anything, as long as the petition is filed on time.
What are my rights when I receive a deficiency notice?
You have the right to see exactly why the IRS made these changes, to respond before any tax is assessed, and to have your case reviewed by the Tax Court if you disagree. The Taxpayer Bill of Rights covers all of this in more detail.
Disclaimer: This article is for general informational purposes only and does not constitute tax, legal, or financial advice. Every situation is different, and eligibility for IRS relief programs depends on your specific facts. Consult a licensed CPA before making decisions about your tax debt.