Everyone ranging from my mother to one of our pro athletes coming off knee surgery is warned about one thing; don’t squat with your knees past your toes. I agree, why would you want to pursue flexibility and strength at the same time? It is just too efficient.
Full squat depth can be described as descending all the way down until your calves touch your hamstrings, and generally involves the knees traveling past the toes at the bottom position. Antagonists argue that this position increases joint stress, particularly at the knee. With most of our new athletes, it is painful to get the proper depth because our hips are so tight from sitting at the computer, playing sports aggressively, and worst of all; aging. The squat can be a dangerous exercise when performed incorrectly, whether it is this hip inflexibility or the athletic egos that prod us all to put too much weight on the bar. However, the benefits yield far greater results than any other exercise.
A 2003 study out of the University of Memphis examined squats under 2 different conditions, one group restricted forward shin movement (i.e. keeping the knees behind the toes), while the other allowed subjects to squat normally, pushing the knees past the toes. The researchers found that restricting the movement of the knees over the toes increased the forward lean of the trunk and inward deviation of the knees, resulting in a 22% decrease in knee torque and a 1070% increase in the torque placed on the hip and low back. Another study out of the University of Southern California have added to these findings of increased hip/back stress, but discovered no difference in knee stress on varying depths. So the safest method of squatting is to focus on technique, as this lift is a skill like anything else.
On your descent, keep your chest up, your heels on the floor, and go as deep as possible (ignoring wherever your knee position ends with regard to your ankle). As you get comfortable, continue to increase the weight. But if you’re competing against our athletes, please avoid squats or perform them only halfway down, as exercise must be inefficient, never simultaneously improving both strength and flexibility. Fry AC, Smith JC, Schilling BK. Effect of knee position on hip and knee torques during the barbell squat. J Strength Cond Res. 2003 Nov;17(4):629-33.