Why do your muscles hurt when you exercise?

it depends on what you are doing and whether you have been inactive for a long time if you've been inactive for a while it could be that your muscles have microtears - small tears in the muscle that will repair itself within a few days - your body does this to ensure it is working in the most effective way if you have not been inactive for a long time perhaps you were working at a very high intensity and have experienced lactic acid build up, which is actually a build up of protons causing your muscles to become acidic.