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The rules for filing a claim for refund with the IRS and State tax agencies are straight-forward.  For the IRS, the claim (Form 1040X or Form 843 for employment and certain other taxes) generally must be filed within three (3) years of the due date of the return, or two (2) years from the date of the last payment, whichever is later.

For the California Franchise Tax Board, the claim (Form 540X) must be filed within four (4) years of the due date, or one (1) year from the date of the last payment.

Here is a link to a discussion of the FTB rules on filing refund claims.