In 1961, Karl Klein, from the University of Texas, published a paper showing that deep squats loosened the knee ligaments (J Assoc Phys Ment Rehabil, 15: 6-11, 1961). Based on this study, the American Medical Association recommended against deep squats. This paper caused several generations of American men to practice ‘curtsy squats’ and leg presses in the gym. Since then, many well-controlled studies showed that deep squats— when practiced correctly— strengthened and stabilized the knee joint. These studies showed that the forces on the anterior and posterior cruciate ligaments in the knee decreased as the knee flexed.
Performance goals should determined squat depth. Squatting to parallel builds the quads best, while squatting lower puts greater loads on the glutes. People with healthy knees can do deep squats, but they are not recommended for people with arthritis or chondromalacia (sore kneecaps). (National Strength and Conditioning Association Hot Topics Reports)