It was Southwest's second losing quarter of 2008 after 16 straight years without finishing a three-month period in the red.
Southwest said Thursday it lost $56 million, or 8 cents per share, compared with a gain of $111 million, or 15 cents per share, a year ago. Excluding charges and other items, it earned 8 cents per share.
That beat analysts' expectations of a profit of 5 cents per share.
Southwest paid 23 percent more for fuel than a year earlier.
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