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Starting sometime last spring I started getting this pain in the back of one of my knees. It felt more like a soreness than anything sharp but it was enough to cause me not to run for fear of doing something worse. I talked to my doctor and they suggested an MRI be done. The results came back with nothing wrong and suggested physical therapy. I got a second opinion with an orthopedic surgeon and was suggested the same thing. Its possible they said it was a form of tendonitis. I went through the therapy for about a month and eventually I was able to run pain free on a treadmill for a short time then the pain came back. I continued the therapy at home and tried again and the pain once again returned. I read up on barefoot shoes so I got a pair and after walking in them for a month I started running on a treadmill and everything was great. I kept up with it for a couple more months adding hills to the mix and still everything was good. I decided to try going outside with them running about a mile. The route I chose had a hill so half the trip would be uphill and the other half downhill. The pain returned once I started running downhill.
So what I would like to know is could there be a problem with my stride? It seems like the common factor here is the downhill element as even now I am able to run uphill and on flat ground via a treadmill painfree after getting hurt again a couple weeks ago. The shoes don't seem to matter (regular sneakers or minimalist shoes) as the pain returns regardless of which I wear although I can't run at all anymore in regular sneakers. Is there anything I can wear on the knee itself that'll help with this? I really want to be able to run outside again so any input would be appreciated.
You might have "nothing wrong" with the internals of your knee joint, but there could be some differences in the way your knee is structured that have allowed for hyperextension of the knee joint, which could result in tiring and/or chronic pain in some of the muscles that stabilize the joint. This would not show up on the MRI. Are you hyperflexible or "double-jointed?"
When you say the problem is more evident when you go downhill, this is probably while you decelerate. You see, the problem I detect here is that you said "knees," not "knee." While this doesn't completely rule out an old injury, it makes one highly improbable as an explanation for bilateral pain. The first thing I'm wondering, is if it has something to do with anterior cruciate ligaments, there would be a pronounced difference in muscular compensation when going downhill. This might not be noted on an MRI either.
On the other hand, there are a couple of muscles on the back of the knee and some close to the knee that can produce a sensation of pain there. The former might be involved in compensation if there was rotation of the knee joint due to some problem in the foot or hip that required this repetitive movement. The latter could be sensitive to an ACL deficiency by altering the muscle firing sequence, or sensitive to the tendency to heel strike downhill. Note the Popliteus muscle and tendon below (kneesurgery.com). Test for problems with this muscle/tendon by laying face down with lower leg (tibia) internally rotated (toe in), then knee flexed against resistance.
Let's go with the best case scenario, since the worst case will no doubt be explored by your doctors. Suppose you are heel striking downhill because of the angle change, which would come under the category of "gait" or "stride.". Maybe supporting muscle, like your upper calf muscle Gastrocnemius, or the hamstrings, are producing the pain in back of your knee, which they are known to do. This could be captured by a slo-mo video analysis, if downhill running can be simulated on a treadmill or captured outdoors.
There have been bizarre cases of bilateral bakers cysts reported that were due to chemical changes in the body from another underlying disease, but this should have been revealed by an MRI, as well as bursitis or varus thrust. You may have another explanation revealed by a complete health history, explaining strain causing invisible myofascial pain in the area. There are also spinal/sacral causes that would require another scan.
While some people swear by straps and such (I've tried some), their advantage is mostly psychological. There are some mechanical types out there that are structural, but they are very expensive. Here is a report from the inventor of Kinesio tape on improvement of circulation to heal Popliteal injuries, if that is indicated...http://www.sportmedicine.ru/articles/changes_in_the_volume_of_the_peripheral_blood_flow_by_using_kinesio_taping.htm
This may be overly-simplistic, but have you considered or tried a knee, ligament or strap brace to reduce pressure and re-distribute/balance the impact? (Maybe even wrapping in athletic tape or ace bandage to help the alignment of your knee during exercise). Also, re-evaluate the amount of stability and pronation control from your footwear.
Hope you are running well soon!