I developed knee pain a few years ago when I increased my training volume on the bicycle. I am not a youngster so I knew from experience (which comes from bad judgment) that it takes me longer to recover now than when I was younger. So I used a three part approach - 1) I had an orthopod look at the knees (several surgeries over the years have been inflicted on them!) and we decided to have a series of Hyaluronan (also called hyaluronic acid or hyaluronate) shots which might improve the wear surfaces somewhat (and it has lasted about two years so far!); 2) I used a Physical Therapist to work on muscle and alignment issues for the knees - the PT's I used were also USA Cycling Coaches so they really knew about bicycle related injuries and not just general stuff; and, 3) I used the PT's to actually do a bike fit based on my specific biomechanics (in this case we needed different pedals and width positioning to get alignment of my hips, knees, and feet which the bike shop fit didn't address). So depending on the severity of your knee pain and the history behind it, you might consider some of these kind of approaches as well. Small imbalances can really come back to bite you in biking - I calculated that on a recent multi-day trip, that I turned the cranks at least 225,000 times - a small misalignment pain can get magnified with high cycles!

I hate to post "me too" entries, but in this case - i'm going to agree with what everyone else says - "GO GET A BIKE FITTING DONE". In the past I've had a couple of custom frames made, before the advent of Carbon Fibre and compact frame geometry, it was pretty much "De Rigeur" to do so... especially for people who are a funny shape like me - short legs long torso. Over the years, I've grown so accustomed to my bike layout, I'm sensitive to a 2-3mm drop/raise in my saddle height, and if my pedal cleats are even a fraction out I can tell within 100 yards. Go get measured, get a bike fit done, and measure every thing that's measurable on the bike, record it, and check it every 500 miles/once a month, as part of a routine maintenance program.

for me my knee pain came from my clips. I was using Shimano that had little free play in them. When I got to thinking about the pain in my knee I quit using the clips. The pain went away and when I started using the clips again the pain came back. So I switched to Speed Play Zeros and don't have the pain anymore. Also I agree with the others that a good fit is well worth the money.