If it doesn't hurt when you do body weight squats with zero weight, then you can make it not hurt when you do heavier weights. The trick is to start with body weight squats, or an empty bar, and build slowly. At every step, keeping proper form. Adding only 5 lbs each workout. So many people make the exact claim you're making, without actually going through the painstaking process of starting from no weight on the bar and moving up over a period of a year. You may actually have a real problem in your knees, but if you can do body weight squats without pain, you can work up from there. If you can sit down in a chair without your hands, you can probably work up from there too.

I had problems with my knees after I gained a heap of muscle and then levelled out on my weight and stopped squatting for a while. My knees were now sore all the time.

At some point I read an article called "Everything you know about fitness is a lie" (which has been posted to HN several times), which has a section entitled, "You're only as strong as your weakest muscle". It talks about strengthening stabiliser muscles and exercises to rehabilitate weakened muscles.

The section also illustrates some of the better exercises you can do to alleviate injuries. In particular, there is an exercise for strengthening the knees - I can only describe as a straight leg lift while lying on one's side - which I tried for a couple of weeks, despite the flak I copped from my weightlifting compatriots.

I believe it works the quadriceps, and from my research, the exercise alleviates the difference in strength between the hamstring and the quadricep (don't quote me on this though), which seems to be the cause of my particular joint problem.

However, I've found I can't just go up to a certain point and stop the exercise. I need to continue with it as long as I'm doing squats. It's annoying, because none of my weightlifting crew have this problem, so I think it's got to do with the particulars of my genetics, but whatever works.

I used to have patella tendinopathy in one of my knees from heavy squats. I was able to eliminate all pain in about a week or two using these "Voodoo Floss Band" things.[1] They don't seem like they would work that effectively, but calling them magical is as justified as it was for the iPad. I had tried other strategies such as decline boards and negatives for several months which are commonly prescribed by physical therapists but they didn't make much of a difference. After my knees were 100% from the bands, I began squatting heavy weights again and focused more on keeping my knees out and my butt further back. This seems to have resolved my issues and I no longer experience knee pain squatting (my 1RM is >350).

1: http://www.mobilitywod.com/2012/05/voodoo-band-your-patella-...

In the absence of pre-existing knee issues I would wager that there's something wrong with your squat form. Do you squat below parallel? Do you sit back with your weight on your heels and spread your knees apart when squatting? Have you tried taking a video (from the side) of yourself barbell squatting and posting it to one of the major lifting forums for a "form check?" You can get a lot of good form/technique feedback that way.

There is very high chance that you were not performing squats properly. Tiny deviations in squat form can mean the difference between a PR and knee pain for me.

Could be the meniscus. MRI might help to figure out what is going on. Just my 2 cents.

Where is the knee pain, what type of squat are you doing and to what depth?

Are you sure you're going below parallel on your squats?