What causes that cramp in your side during exercise? It turns out that scientists don't actually know. There have long been two prevailing theories. The first is that it comes from a cramp in your diaphragm, the muscle that enables your lungs to fill with air. This may seem likely on its face, but it doesn't hold up when you think about the fact that side aches are a common ailment of horseback riders, who aren't breathing heavily when it happens. The second theory is that the pain comes from a jostling of your organs during excessive movement. This doesn't really hold up either, as anyone who has had a side stitch can tell you it's in a single area, not all over.