Runner's knee happens when the kneecap (patella) tracks incorrectly over a groove in the thighbone (femur) known as the femoral groove when you bend and straighten your knee. In healthy knees, the patella rests in the femoral groove and slides easily up and down when you use your knee. But when the patella is out of place, it can irritate the femoral groove and wear away the cartilage beneath the patella, leading to knee pain.
http://kidshealth.org/teen/food_fitness/sports/runners_knee.html#cat20134