A related discussion, knee pain was started.
Three possibilities:
1. ITB (Iliotibial band Syndrome), which is caused by friction of th ITB over the lateral femoral condyle. Usually responds to stretchng, ice, NSAID's, and occasionally orthotic inserts
2. Patella Femoral Syndome, also known as "runner's knee" this has a variety of causes but is usually improved with Physical therapy, NSAIDs, correction of shoe wear. Occasionally surgery is needed
3. Torn lateral meniscus. Usually requires surgery.
If the pain is persistant or worsens, I would recommend orthopedic evaluation.