Audit Time Limitation. Most taxpayers who file a complete and accurate tax return before the filing deadline can be audited by the IRS within three years of the filing deadline. For example, even if you file your tax return before the April 15 deadline, the three-year period doesn't begin until April 15.n the unlikely event you are chosen for an audit and the IRS increases the amount of tax you owe, you may be responsible for interest and penalties on that amount. For example, if the increase in tax is due to a negligent mistake you make, then the IRS will charge you 5 percent of the underpayment as a penalty.