What shoes are you running in? Are they older ones - if so, they might be worn out and you don,t have any cushioning in them. Are they the right ones for you? Do you need cushioning, stability or motion control?

Can I suggest you take your runners into your nearest running specialty store and get them to take a look at them and make sure they are still supporting/cushioning your and they can also take a look at your gait and make sure they are the right kind.

Its amazing what running in the wrong shoe can do to your knees. Something to think of.

Hope they clear up soon!