A system and method are provided for in vivo, noninvasive diagnosis of patellar and scapular malalignment and maltracking. The patellar system and method include a patella-engaging apparatus and a motion analysis system. The patella-engaging apparatus includes a member that has a custom-contoured posterior surface that is configured to engage an anterior surface of a subject's patella. A plurality of markers is coupled with the anterior surface of the member and the motion analysis system optically tracks the plurality of markers. The system and method may optionally include a second portion such as a goniometer that tracks relative movement of the tibial and femoral portions of the subject's leg proximate to the patella. The member that has the custom-contoured posterior surface may be employed in a method and system for treating malalignment and maltracking, and a method for evaluating the effectiveness of treatment of the same.