Preclinical studies of bone repair remain a high priority because of unresolved clinical problems associated with treating critical segmental defects and complications of fracture healing. Over the last decade, the murine femoral allograft model has gained popularity due to its standardized surgery and potential for examining a vast array of radiographic, biomechanical, and histological outcome measures. Here, we describe these methods and a novel semiautomated histomorphometric approach to quantify the amount of bone, cartilage, and undifferentiated mesenchymal tissue in demineralized paraffin sections of allografted murine femurs using the Visiopharm Image Analysis Software System.