A system and method is disclosed herein for measuring alignment of the muscular-skeletal system. The system comprises a sensored module that can be placed within a prosthetic component to measure load, position of load, and joint alignment. The system further includes a remote system for receiving, processing, and displaying quantitative measurements from the sensors. Alignment relative to a mechanical axis is measured. In a two bone system with a joint therebetween the total alignment measured comprises offsets measured for each bone. The joint is placed in a predetermined flexion that supports measurement of the joint as it is moved. The joint pivots on a point that is along the mechanical axis. Points along the arc made by the joint rotating between a first and second point are measured. An arc maximum is determined. The arc maximum is then converted to varus or valgus offset relative to the mechanical axis.