I'm pretty cognizant of my form while running but I know that I'm not nearly as consistent as I'd like to be. I feel as though I have a pretty straight gait and that I'm not too wobbly while running so I believe my knees are not being asked to do much more than their normal functions. However, at the end of a long run, all I want to do is stretch my knees somehow. When I squat up and down that seems to help, but I don't know that it's actually stretching anything. Going up and down stairs after a long run is a true chore. I have to go slow and hold the handrails. The pain doesn't last long but it sure is uncomfortable. I'm working on a series of running Q&A answers for a blog, www.healthandrunning.com and would appreciate any information or insight you can provide.
Sorry to hear you are having problems with your knees! Have you been fitted for running shoes? How old are your shoes? They may be the problem. A reputable running store will have qualified staff to analyze your gait and recommend the most appropriate shoe (neutral, support, guidance). If your shoes are older (6 months +), the cushioning may have deterioted and not providing you with the support you need. Unfortunately I don't know of any specific knee stretches. Have you checked Runner's World online? They have a ton of exercises for every part of the body. Good luck!
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