Seeing a doc is a good idea. Meanwhile, look at information on Iliotibial band syndrome. Are you toeing in excessively while you pedal? The feet should be straight ahead or possibly slightly angled outward for best knee flexion biomechanics. The seat should be high enough, and the top tube the right length with the seat set back just right.
http://en.wikipedia.org/wiki/Iliotibial_band_syndrome