Overpronation
When you run, as your heel strikes the ground your foot rolls slightly inward to help cushion the force. This is called Pronation. Overpronation is when your foot rolls inward too much. Also be aware of Supination which is the exact opposite; when your feet don't roll inward enough. Supination has a good chance of leading to stress fractures and really bad heel pain.
Causes
The causes of these problems stem from genetics and poorly learned technique that probably started when you were learning to walk or shortly after. This condition can turn into a really uncomfortable one as your feet will get sore pretty quick, and you will get fatigued faster than usual.
Treatment
Many runners and athletes have this problem and there are many types of special shoes available to help you out. Getting soles in your everyday shoes will help if your feet tend to get sore quick, but for exercise and sports you will definitely want some special shoes for your problem.