One of the most frequent injuries in subjects who practice sport is the rupture of the anterior cruciate ligament (ACL). Appropriate reconstruction and rehabilitation are key issues in full recovery of patients and their return to previous activities. This paper presents a new method to estimate muscle strength during a dynamic exercise from kinematic and electromyographic (EMG) data. Recovery of patients with ACL rupture and reconstruction was evaluated 4 and 6 months after surgery by assessing the differences in knee extensor and flexor muscle activity between the unimpaired and injured limbs. The results show that squat EMGs from the extensor muscles of the knee from the injured and unimpaired limb could help assess rehabilitation outputs in patients who had undergone an ACL reconstructive surgery.