This is a very difficult question. If the pending audit changes will affect this year’s tax return it may be advisable to wait until the audit has concluded before you file for this year. Sometimes there are urgent reasons why you must file this year’s tax return even though the audit has not yet concluded including loan applications, car loans, mortgage refinance and student loans.  In that event, you may need to file an amended tax return after the audit has been concluded. If you can wait to file this year’s tax return until the audit has been concluded, don’t wait too long. Any refund listed on this year’s tax return may be barred by the refund statute of limitation if the tax return is not filed within three years of the due date plus any extensions.