banerjek is right, please don't rely on our diagnosis here in the forum...

You mentioned your knee pain is in the middle. So, is that middle of the knee cap, or is it the tendon that goes from the kneecap to the tibia? If you don't get this playing football, it is more likely to be the seat height/position. I would take your bike into a shop and get them to double-check your position. Knees are not something to be trifled with. If you get set up at a reputable local shop and you're still having problems, stop riding and see a physician.