You need to be more specific about what actually hurts when you run? Is it your knees, you shins, your ankles? Anyway, if you have just started working out again it may take a little while for your legs to get back into working condition. When I first started running again, after about a month I had to take about 3 weeks off because of pain in my right knee. When I came back, I made sure to throw in alot of low impact cardio so that I could slowly work my way up to running a few times a week. I think that it is very important to let your legs acclimate to your workout. If you can use an elliptical, bicycle, or walk on a treadmill, I would suggest doing this at first. Also, of course, if the pain is persistent, and does not go away I would suggest seeing a doctor.