Filing separately doesn't help when it's time to balance the books, either. Couples filing jointly can deduct $3,000 in capital losses against ordinary income. Those filing separately, however, can deduct only $1,500 in losses and can't use one spouse's losses to offset another's gains. It's a big reason why only 4.5% of married couples filed separately in 2009, the last year for which data were available. Married couples filing separately made up less than 2% of all returns filed that year, but that didn't necessarily mean they were making the wrong call.