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http://taxes.about.com/od/filingstatus/qt/marriedseparate.htm

The editors of JK Lasser's Your Income Tax advise:

"If you suspect that your spouse is evading taxes and may be liable on a joint return, you may want to file a separate return. By filing separately, you avoid liability for unpaid taxes due on a joint return, plus penalties and interest."

In other words, on a separate return, the taxpayer will be responsible only for the accuracy of that tax return, if audited, and will be responsible for paying the tax on that return (or any additional tax that results from an audit).