I have been running since January 2012. (about 2 years now) In my freshman year, I joined track after a season of soccer at my high school because I had always enjoyed running. We were doin 2 track workouts a week with 3-6 mile runs on the other days. I dealt with shin-splints for much of the season, but now that is behind me. Track ended and I joined cross-country. I immediately increased miles. I was running 6-10 miles per day, now I realize this was too drastic of a change. My toes and ball by my big toe began hurting badly and eventually my lower knees (on top of my shin-bone) began hurting too. I went to physical therapy, became more flexible, and strengthened. I rested for 2 weeks. A week ago I started running again. After a week, my lower knees are hurting again. Has anyone experienced this or have a diagnosis or know what I can do to stop this? I'm 15, 145 pounds and 6' and have grown a lot in the past year, if that helps at all. 

So, lower knee pain at the top of my shin. It gets worse with running.

Thanks.

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This might be an easy fix to relieve the pain. Try stretching your quads before and during your running. Your quads are tight and pulling on your knee not allowing it to track properly.
I would also look at your cadence as it might be too slow and you might be keeping your knees bent too much in general placing stress to the quads making them tight and causing some of the shin issues.
If it is from tight quads the pain relief will be instant but again eventually you must remedy the reason for the tight quads.

The area you describe as the source of pain in tandem with the fact it flared up immediately following a sharp increase in mileage leads me to think it could be a case of patellar tendonitis. You're quite young and have undergone a growth spurt recently so it could also be Osgood Schlatter. Either way, I'm just going to echo Eric and say that quad stretching is fantastic for relieving knee pain in my experience. That aside I think you're just going to have to reassess your form and get plenty of rest.

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