If the IRS believes that you owe more tax than what was reported on your tax return, the IRS will send a Notice of Deficiency explaining the additional tax due and how the amount was calculated. Included with the Notice of Deficiency will be Form 5564, Notice of Deficiency Waiver, which the IRS asks you to sign and return to them.
If you disagree (either partially or completely) with the proposed additional tax due, then you should NOT sign Form 5564. Form 5564 should be signed and returned to the IRS only if you fully agree with the additional tax due.
Taxpayers who disagree with the additional tax assessment have 90 days (or 150 days if the taxpayer lives outside of the U.S.) to resolve the matter. There are no extensions to the ninety-day window. As a first step, you may want to submit a letter to the IRS stating why you disagree with the notice, and include with your response copies of any documentation supporting your position. If you have not been able to resolve the matter with the IRS and the ninety-day window is close to expiring, you will want to submit a petition to Tax Court to challenge the deficiency assessment.
