Squatting is a common strength training exercise used for rehabilitation, fitness training, and in preparation for competition. Knowledge about the loading and the motion of the back during the squat exercise is crucial to avoid overuse or injury. The aim of this study was the measurement and comparison of the kinematics of the lower leg, trunk, and spine during unrestricted and restricted (knees are not allowed beyond toes) squats. A total of 30 subjects performed unrestricted and restricted barbell squats with an extra load of 0, 25, and 50% bodyweight. Motion was tracked using a 12-camera Vicon system. A newly developed marker set with 24 trunk and 7 pelvic markers allowed us to measure 3D segmental kinematics between the pelvic and the lumbar regions, between the lumbar and the thoracic segments, and the sagittal curvatures of the lumbar and the thoracic spine. In an unrestricted squat, the angle of the knee is larger and the range of motion (ROM) between the lumbar and the thoracic segments is significantly smaller compared with a restricted squat (p < 0.05). The studied subjects showed significantly increased ROM for thoracic curvature during restricted squats. The unrestricted execution of a squat leads to a larger ROM in the knee and smaller changes in the curvature of the thoracic spine and the range of smaller segmental motions within the trunk. This execution in turn leads to lower stresses in the back. To strengthen the muscles of the leg, the unrestricted squat may be the best option for most people. Thus, practitioners should not be overly strict in coaching against anterior knee displacement during performance of the squat.