Last fall I went for a long run that was admittedly more than I should have been doing. I felt fine on the run but the next day I could barely put weight on my right leg or extend it. I had pain on the inside of my knee, above my knee and up the inside of my leg. I took a couple of weeks off and the pain subsided. I went for a short run and was again in pain the next day and for a couple of weeks. After a couple of more attempts at rest and having the same problems I eventualy went to my GP and he said rest for many months. I have now not run in 6 months and I went for a .5 mile jog and I am right back where I started. My GP did a bunch of twisting tests that he said rules out a ligament problem. I have no swelling or catching of the joint to indicate a meniscus problem. If this were bursitis or a simple pull I would have thought it would subside by now or at least swell up on me. I just get this horrible pain on the inside of the knee, not in the knee, and the pain then spreads to the area of where my quad tendon connects above the knee and farther up the inner hamstring muscle. To me, it feels like I have damaged several muscules and/or tendons around the knee and can't seem to get them healed. Can anyone think of ways to rehab this or at least give me an idea of what it might be?
Go and see a good musculoskeletal physiotherapist. It sounds to me like you might have an imbalance in your quads causing your patella to track unevenly when you run (surprisingly common) or an overpronation causing stress to your knee, but there could be any number of causes for what you describe. You called your doctor a GP which makes me suspect you are in the UK - where exactly are you?
Honestly, for the sake of £40 or whatever I'd shell out and see a private physio - many physios attached to football and rugby clubs also run private clinics, and they're usually far more familiar with athletic injuries than the granny-draggers working for the NHS. With the best will in the world GPs can't be experts on everything, so a good sports-experienced physiotherapist may be the best bet - it may be worth asking to have your gait pattern analysed to check for imbalances too.
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