Originally Posted by SHELDON BROWN

Knees
Cycling, done properly, is much less stressful to the knees than many other aerobic activities, since there's no impact involved. Nevertheless, knee injuries do occur, usually as a result of poor technique or position.

Gear Selection
A principal cause of knee problems is over-stress as the result of using too high a gear. For more on this, see my article on Gear Shifting.

Saddle Height
Another common cause of knee problems is incorrect saddle adjustment, particularly if the saddle is too low. See my article on Saddles for more details on this.

Cleat Adjustment
Some knee problems result from incorrect placement of shoe cleats. Everybody has a natural angle that each of their feet prefers to be at; some are duck-footed, some are pigeon-toed, whatever. When you walk or ride with plain pedals, your foot assumes this angle, and everything is hunky-dory. If you use cleated shoes and matching pedals, it is important that the cleat is adjusted so as to permit your foot to be at its natural angle. If your cleats are misadjusted, the resulting twist on your lower leg will affect the alignment of the knee joint, and cause serious problems.
This is less of an issue if you ride pedals with "float" (limited rotational freedom) in the cleat attachment. Most newer clipless pedals offer at least some float.

The N.E.C.A. Fit-Kit © includes a cleat adjustment procedure called the "R.A.D." (Rotational Adjustment Device) which is very worthwhile for "problem" cleat fittings.

Lateral Movement--Chondromalacia
The knee joint is basically a ball-and-socket joint, with the ball at the bottom of the femur and the socket at the top of the shinbone. A common cycling-related injury is called "chondromalacia", and has to do with irritation of the cartilage pad in the "socket" which provides lubrication for this joint. Reputedly, an edge of this cartilage can get turned up and dog-eared, causing irritation and inflamation.
Chondromalacia is often blamed on lateral movement of the joint, and a common prescription is to strengthen the quadriceps muscles which run along the front of the thigh and along side the front of the kneecap. It is these muscles which provide lateral positioning for the joint. The usual exercise prescribed for this is to sit in a chair with one leg at a time held out straight, unsupported. Sometimes it is suggested to place a pillow or other weight on the foot for this exercise.

Something the doctors don't seem to think of suggesting, but which really helped me a lot, is to make a concious effort to avoid lateral knee movement during the pedal stroke. Watch your knees as you ride (in a low-traffic setting!) They should move up and down as you pedal, with no sideward motion. Many cyclists have a sideways hitch in their pedaling motion, which I believe is a major contributor to chondromalacia. If you pay occasional attention to this, it doesn't take long to train yourself to keep the knees in line.


Long Cranks
The longer your cranks are, the farther your knees will have to flex on each stroke. Different riders will have different amounts of flexibility in this regard, but riding with longer cranks than you are used to can definitely cause problems.