Why do my knees hurt when I squat?

Brett and I were having a conversation this week about knee pain and he was saying that, in effect, if knee pain can't be recreated by specific tests or stimuli, and if it comes and goes or can be affected by pressure or compression on the knee, then it probably isn't a specific pathology and probably isn't something to worry about. So where does that leave the average person who has ruled out serious pathology and wants to squat without knee pain? The main things that can positively affect knee pain like that are loading and graded exposure. Tendons and ligaments need to be put under load to adapt and strengthen, which is how we reduce knee pain and improve function. While doing this, easing in to exercises that may not feel comfortable is the easiest way to adapt your internal structures and tolerance for various movements. Brett had me try a squat with my back on the wall, heels up on the wall. I have long legs and initially my knees did not like how it felt. Within a week or two I was able to do the motion without pain. I don't think that I had a major adaptation to my tissues in that time, I think I just used some graded exposure to build tolerance which allowed me to perform the exercise without pain. I started slow and just a few reps a day and built up. This is how you can handle any exercise that doesn't feel the best initially. Try it with deadlifts for your back, squats for your knees, lunges for your knees or whatever else you want to be able to do. Pain does not mean damage!

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My knees hurt or back hurt after running/ exercise, what should I do, when should I be concerned?