The temporomandibular joint (TMJ) is a specialized synovial joint that is essential for the movement and function of the mammalian jaw. The TMJ develops from two mesenchymal condensations, and is composed of the glenoid fossa that originates from the otic capsule by intramembranous ossification, the mandibular condyle of the temporal bone and a fibrocartilagenous articular disc derived from a secondary cartilaginous joint by endochondral ossification. However, the development of the TMJ remains unclear. In the present study, the formation and development of the mouse TMJ was investigated between embryonic day 13.5 and post-natal day 180 in order to elucidate the morphological and molecular alterations that occur during this period. TMJ formation appeared to proceed in three stages: Initiation or blastema stage; growth and cavitation stage; and the maturation or completion stage. In order to investigate the activity of certain transcription factors on TMJ formation and development, the expression of extracellular matrix (ECM), sex determining region Y-box 9, runt-related transcription factor 2, Indian hedgehog homolog, Osterix, collagen I, collagen II, aggrecan, total matrix metalloproteinase (MMP), MMP-9 and MMP-13 were detected in the TMJ using in situ and/or immunohistochemistry. The results indicate that the transcription factors, ECM and MMP serve critical functions in the formation and development of the mouse TMJ. In summary, the development of the mouse TMJ was investigated, and the molecular regulation of mouse TMJ formation was partially characterized. The results of the present study may aid the systematic understanding of the physiological processes underlying TMJ formation and development in mice.