"Finally, the Big Question: Does e-filing raise the chances of an audit? There isn't any hard evidence either way. Some e-filing fans, like Doug Stives, a CPA from Red Bank, N.J., think it keeps taxpayers "below the radar." But a 2009 report from Congress's Joint Tax committee linked e-filing to a higher overall audit rate, saying the cost savings made the IRS "better able to make use of its computer infrastructure to target returns with audit potential."

From here: