Day 14 ICR mouse first lower (M1) and upper molars (M1) as well as heterotopic recombinations of M1 epithelium/M1 mesenchyme and M1 epithelium/M1 mesenchyme were cultured for 6, 8 and 10 days on semi-solid medium. Computer-assisted 3D reconstructions were performed to follow the in vitro development of these explants. In vitro culture of cap-stage molars allowed for the emergence of unequivocal morphological features distinctive for M1 versus M1 including the cusp pattern, cusp inclination and tooth specific chronology for odontoblast and ameloblast terminal differentiations. Both M1 epithelium/M1 mesenchyme and M1 epithelium/M1 mesenchyme recombinations developed according to the known developmental fate of the mesenchyme. Our data demonstrate that the cap-stage dental ecto-mesenchyme not only directs tooth class specific morphogenesis, but also individual molar crown features. Furthermore, the mesenchyme apparently also controls the typical mirror symmetry of right and left handed teeth.