Welcome to the wide world of women diagnosed with chrondro-whatsit and patellar alignment issues.
For patellar alignment, one issue can be that if you don't fully extend your leg, the inside quad doesn't fire (at least, this is what a PT told me). In cycling you don't lock out your leg, so your outer quad gets stronger and contributes to the issue. So cross-training may help you. One exercise is to stand on one foot on a step, the other foot hanging off the lower side. Slowly lower yourself so that your knee is bending, then straighten up again, making a point of fully straightening the leg. Two or three sets of 10-15 ...
Also, stretching the IT band is key. If you can stand the pain, some massage work on the IT band may help; it's painful, but good. You can get some of the same effect by rolling the outside of your hip over a foam cylinder. If it hurts, you're doing it right.
There are other exercises; I don't remember them off hand, though. Most of my knee issues have gotten a lot better in the last few years, and I'm not really sure why, although I suspect it has to do with getting into a variety of different activities rather than just riding my mountain bike. Hiking can be a bear, still, though, and after playing two and a half hours of indoor soccer yesterday (normal game is one hour), my knee is definitely talking to me (mostly saying that I need to build up my lateral stabilizers before trying that again).



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