The aim of this study was to quantify bone microarchitecture within the glenoid fossa and mandibular condyle following mandibular distraction osteogenesis. Eight 6- to 9-month-old male beagle dogs underwent bilateral vertical mandibular distraction with semiburied distractors (12 days of distraction at 1 mm per day). One unoperated animal served as control. After distraction the animals were divided into two groups (N = 4) and killed after 1 or 2 months of consolidation. Three-dimensional trabecular architecture was analyzed by micro-computed tomography (μCT). At both sites the overall trends were similar. In the glenoid fossa, there was decreased bone volume, trabecular number, and connectivity density and increased trabecular separation at 1 month and decreased trabecular thickness and increased structure model index compared with the control (P < 0.05). In the mandibular condyle, there was decreased bone volume, trabecular number, and connectivity density at both 1 and 2 months, with decreased trabecular thickness and increased structure model index at 2 months only compared with the control (P < 0.05). The bone became less dense and more rodlike. These bone changes are similar to those seen by the effects of aging or impaired normal function. Thus, in the short term, changes occur in the bone microstructure of the glenoid fossa and mandibular condyle after vertical mandibular ramus distraction in the canine model.