The functionality of the dentition depends on occlusal relationships between opposing crown surfaces. To investigate the relative changes in positioning of upper and lower molar germs during mouse development, we used serial histological sections of late day 13 (embryonic day (ED)13.5) to early day 18 (ED18) foetus heads and performed computer-aided 3D reconstructions. From ED13.5 to ED15.5. the first lower molar (M1) got a less medial position relative to its upper counterpart (M1); superimposition progressed postero-anteriorly. From ED14.5, the apparent medial displacement of M(1) vs. M1 was partly due to the asymmetrical growth of the M(1) to give rise to the lingual row of cusps, conspicuous at ED17. The superimposition of M(2)/M2 along the medio-lateral axis was observed from their bud stage (ED14.5), and the one of M(1)/M1 was almost complete at ED15.5. However, this was not the final position. as at ED 18, M1 and M2 had a more lateral location than their upper counterparts. Immunostaining showed that differential expression of antigens associated to desmosomes but not to adherens junctions might be involved in the asymmetrical development of M(1) thus contributing to the relative medio-lateral positioning of the first molars at early stages.