check engine light

I have a '99 SE. Every now and then, I start it up and it runs rough for about 30 seconds. After 30 seconds or so, the idle goes back to normal. This rough idle, however (aparently) causes the check engine light to come on and stay on for the rest of the day. No big deal since when I start it the next day ( after at least 8 hours of down time ) the engine light is gone. This happens I would say about once every 3-4 weeks. Any idea what it could be ? Thanks