The properties of articular cartilage vary across the surface of the femur in the knee joint. These site- specific properties are affected by mechanical loading patterns, which are altered depending on the state of the joint. For instance, loading patterns are altered when the knee suffers an injury, and this may affect the articular surface in a site-specific manner to initiate or advance wear. The overall motivation for this dissertation was to determine the sites susceptible to cartilage degeneration following joint injury, and the site-specificity required for cartilage repair by osteochondral allograft (OCA) transplantation. To achieve this, a novel robotic mechanical test system (RMTS) and image processing software were developed to investigate the site-specific properties of articular cartilage following anterior cruciate ligament transection (ACLT) in the rabbit, and in OCA repair scenarios in humans and goats. The first objective was to identify sites where structural and functional properties of the cartilage are affected at an early stage in the rabbit ACLT model of joint injury. The RMTS mapped indentation stiffness across the ACLT and the unoperated, contralateral femora, finding the distal, weight-bearing region of the medial femoral condyle (MFC) to be less stiff 28 days following ACLT. The second objective was to investigate site-specificity in the orthotopic match that is the goal in OCA repair. Performing OCA repairs computationally with images of human condyles, the topographic match of non-orthotopic OCA from the lateral femoral condyle (LFC) to MFC recipient sites may be equivalent to that of orthotopic OCA from the MFC. The third objective was to perform the computational OCA repairs on Boer goat condyles. This identified OCA donor locations for testing orthotopic vs. non-orthotopic repair in vivo in an animal model. This work has increased understanding of the topological variation of articular cartilage properties on the distal femur in health, injury, and repair. Knowing the sites susceptible to damage following joint injury, and being able to utilize non-orthotopic OCA for the repair of large cartilage defects have significant clinical implications. Additionally, this work presents technical achievements in producing the semi-automated RMTS and software that performs and evaluates OCA repairs