Generally, the statutory time limit on filing an administrative claim (meaning filed with the IRS, as opposed to in court) for refund is the later of three years from the date the return was filed or two years from the date the tax for that tax year was paid. A tax return claiming a refund is considered a “claim for refund” under this general rule.
If you paid estimated taxes through withholdings or deposits to the IRS, you should be cautious of filing a late return to claim your refund. Even though the administrative claim would be considered timely if you filed your return late, there is an additional limitation to the amount that can be refunded which will render that claim moot. Your refund will be limited to whatever you paid in the 3 years before your late return was filed, plus the period of any extension of time for filing the tax return.
There are a few exceptions to these rules, with the exception for net operating losses (NOLs) probably being the most utilized. Refund claims for NOL carrybacks can be filed within the same 3 year period as the refund claim which has the NOL creating the carrybacks.