This is a controversial topic mainly because for many years well-intentioned fitness professionals, coaches, and rehabilitation professionals observed that many people could not perform a deep squat, or they could not perform it without pain or dysfunction. Accordingly, many experts concluded that since deep squatting in some people produces pain (e.g., in the knees and back), deep squats should be replaced with partial 90-degree knee squats or they should be avoided and machine exercises, such as the leg press, should be performed instead. The problem with this line of thinking is that the deep squat movement is not the real issue. The real issue is that the person has either a stability or mobility dysfunction (or both) and cannot execute a deep squat without improper forces being transferred to the joints (e.g., knees and spine), which ultimately results in pain. That is, excluding musculoskeletal disorders such as arthritis, people who cannot perform a deep squat without pain or dysfunction typically are inflexible due to inactivity or poor body mechanics (e.g., sitting for extended periods and faulty posture) and their nervous system responds to the inflexibility by calling upon compensatory muscles to perform the movement pattern rather than the muscle groups most suited for the job. This creates dysfunction and pain.
In reality, deep squatting is a tremendously functional activity and the human body is designed to do it. Those who cannot squat in a manner that allows the hips to drop below the knees are dysfunctional. To remedy the situation, an exercise program that first promotes stability and mobility all along the kinetic chain and then progresses to dynamic movement patterns should be undertaken. Once the requisite flexibility and motor control are achieved that enables a person to perform a deep squat with his or her bodyweight, a plan for progressing the load through resistance training can be considered.
As always, when an exercise or movement pattern provokes pain in an individual, he or she should get the affected area evaluated by a physician before continuing to exercise.