Core binding factor a1 (Cbfa1) is a crucial transcription factor for osteoblasts differentiation and chondrocytes maturation in embryonic skeletal genesis, but little is known about its function in mandibular condylar growth. The aim of this study was to determine the temporal and spatial pattern of Cbfa1 expression in condylar cartilage during natural growth. Mandibular condyles were harvested from 50 female Sprague-Dawley rats at age of 38, 42, 49, 56 and 65 days. Alcian blue and PAS staining was used for histological analysis. Type A antibody raised against Cbfa1 isoform II was observed in the pre-hypertrophic and hypertrophic chondrocytes in condylar cartilage, and in the mature osteocytes in trabecular bone. Type B antibody raised against 17 aa sequence present after the Runt domain was detected in tartrate resistant acid phosphatase (TRAP) positive osteoclasts in the erosive front of cartilage, and also in the osteoblasts on the sub-chondral bone surface. In situ hybridisation was carried out with a probe containing a fragment in exon 8 of the cDNA. Cbfa1 transcripts were localised in the osteoblasts and chondrocytes, but not in osteoclasts. Quantitative analysis demonstrated that both types of Cbfa1 proteins reached their maximum level on day 56, which coincided with the terminal maturation of hypertrophic chondrocytes and the aggregation of mineralisation deposits in extracellular matrix. These results suggest that Cbfa1 is a master gene controlling the functions of all the skeletal cell lineages by synthesising different functional isoforms. Furthermore, Cbfa1 couples the process of chondrocytes maturation, extracellular matrix mineralisation and degradation, as well as osteoblasts invasion during endochondral bone formation. Beyond its function on embryonic development, Cbfa1 regulates the postnatal growth of mandibular condyle.