This study used a rat model to investigate the microstructural organization of collagen through the transition from scar to intact residual segments of a healing medial collateral ligament (MCL). Twenty-two male retired breeder Sprague-Dawley rats were randomly separated into two groups. Eleven underwent surgical transections of both MCLs and were allowed unrestricted cage activity until euthanized two weeks post surgery. The remaining eleven rats were used as normal controls. All 44 MCLs were harvested including intact femoral and tibial insertions and prepared for scanning electron microscopy (SEM) imaging. At harvest the scar region in the healing ligaments was more translucent than the normal tissue. Ligaments were viewed from femoral to tibial insertions at magnifications of 100X through 20,000X. Tissue away from the scar region in the transected MCLs was indistinguishable from normal tissue in uninjured ligaments. Collagen fibers and fibrils in these tissues were more aligned along the longitudinal axis of the ligament than in the scar tissue. Continuity of collagen fibers and fibrils were consistently observed from the residual portions of the transected ligament through the scar region. Bifurcations/fusions, but no anastomoses, in fibers and fibrils were observed in both normal and scar tissues of ligaments. Qualitatively, bifurcations were encountered more frequently in scar tissue. In the transition region, larger diameter fibers from the residual tissue bifurcated into smaller diameter fibrils in the scar. This connection between larger diameter and smaller diameter fibers and fibrils indicates that bifurcations/fusions are likely to be the dominant way in which force is transmitted from a region with larger fibrils (residual ligament) into and through a region with smaller fibrils (scar).