The aim of this study was to assess the integration of intramembranous and endochondral autogeneous bone grafts into membranous bony defects, by analysing the microarchitectural changes of the grafted bone 3 months after grafting. Twelve critical size defects (15 x 10mm) were created in rabbit mandibles bilaterally. Six defects on the right side of the mandible were grafted with autogenous endochondral bone, and six on the left were grafted with intramembranous bone. Three months later, the defects were retrieved for imaging with micro-computed tomography (Micro-CT) and for radiographic and histological evaluation. Micro-CT showed that intramembranous bone gave more bone volume a larger, trabecular number and trabecular thickness (P<0.001), and that endochondral bone had more trabecular separation (P<0.001). These findings indicate that intramembranous bone grafts integrate better than endochondral bone grafts in three-dimensions when they are grafted into membranous bony defects.