Are you talking about a "stitch"?
If you are, there are many theories on stitches, some say its to do with food digesting, others say its air caught in the diaphram, others that you have not eaten enough and are training too hard at the same time, that its dehydration, lack in a certain vitamin, training too fast for your muscles to keep up with, not stretching or waming up properly....the list goes on.
However, if your talking about a dull ache, then it could be that your putting strain on your core for some reason, maybe start training your core (core stability exercises, balance work, pilataes...etc) and also making sure your posture is in top form when you are exercising. Also stretching everything afterwards so your set up properly to repair whilst you rest and be on top form for the next time you try to run.