Your shoes may not be right for you. Are they worn out? Try going to a Road Runner Sports and see if they can see what type of shoe suits you the best depending on your natural gait/running style/etc..
http://www.dickssportinggoods.com/in...egoryId=222919
This might not be the cure-all but it might help. At stores like Road Runner sports they have treadmills and video cameras that capture the way to run for free.