The short and simple answer is as low as possible. Squatting deeper has not been shown by the research to cause any harm to the knees. The research has actually shown that squatting to 90 degrees puts the most stress and force on your knees, but when you go past 90, there is less force on the knees. If you are someone without any current major knee or other lower leg issues and have the mobility to perform a full depth squat, then by all means, you should. There are several reasons for this. Our joints all have their ranges of motion that they move through. For example, the knees bend and straighten between 0 – 135 degrees (generally). Our muscles, of course, bring our joints throughout those ranges. So when we are exercising throughout the full range, we are strengthening our muscles throughout that full range. So if you truly want to strengthen your lower body and legs, then you want to be strong throughout the full range that your body can squat. If you are only performing partial squats, such as to 60 degrees, then you will only be strong within that partial range. When you are at a lower depth, more muscles are activated and recruited, so you are strengthening even more muscles of the lower body and legs. Squatting deeper will help increase athletic performance such as jumping, and with day-to-day activities, such as getting up from the floor and lower chairs.
Now for the more complicated answer. There are instances when someone cannot squat deep. People with injuries and post-surgery will of course have to be careful with how low they squat. Someone just starting to perform squats will not have the motor control, mobility, and strength to go fully down. Some people naturally will not have the mobility to perform a full depth squat without compensating with some part of the body. While mobility is something that can be worked and improved on, there can still be limits for some. What this means is that there is no straightforward answer to how deep you should squat, but rather how low you go depends on what your body is able to do without putting yourself at injury risk to your back or other body parts. While the goal is to be able to go as low as possible, you only want to do so within a safe limit. It is important you assess and listen to your body to find out what your body is capable of. Every person’s body is unique and different, and thus, our approach to how we treat and exercise should always be individualized and tailored to what fits each unique individual.