individual cyclist anatomy may contribute to knee and hip pain. Cyclists with leg length discrepancies may develop knee pain as only one side is correctly fitted to the bicycle. This leads to increased stress inside the knee and hip joints on the improperly fitted side. Cyclists with flat feet may be more prone to excessive pronation (internal rotation) of the lower extremity causing greater stress on the IT band at the knee. Orthotics (anatomic shoe inserts crafted by podiatrists) may correct the alignment of the knee and decrease or prevent medial or lateral rotational stress on the connective tissue of the ankle, knee or hip, thus reducing the pain.

from: http://www.roadcycling.com/training/kneepain.shtml