Ossification during distraction osteogenesis can be classified as intramembranous or endochondral. It is not known whether cartilage in the distraction gap is transformed into new bone. The aim of this study was to investigate the morphological features of ossification in the transition of cartilage to bone during mandibular distraction osteogenesis in a rabbit model. A cortical osteotomy was performed and custom-made devices were applied. Immediately after surgery, the devices were lengthened by 0.25 mm every 12h for up 10 days, during which time four rabbits were killed at 0, 5 and 10 days and examined using histological staining and immunohistochemical methods. Apoptotic cells were identified by an in-situ detection assay for nuclear DNA fragmentation using a modified TUNEL procedure, with several sections analyzed using software for histomorphometric analysis. The results showed that the amount of cartilage in the distraction gap was significantly decreased. The cartilage had ossified in two ways, termed endochondral ossification and transchondroid bone formation.