The secondary palate formation in mouse has been associated with the period of fast growth of the mandible from embryonic days (ED) 13.0 to 16.0. During that time, the incisors and first molars develop from the bud to the bell stage. We investigated the position and growth of the tooth during prenatal elongation of the lower and upper jaws, and searched for the developmental stage when alignment of opposing teeth was achieved. Computer-aided 3D representations allowed us to represent the position of incisors and molars in the embryonic head from ED 13.5 to 18.0 on the basis of data obtained from histological sections. The atlas-hypophysis connection exhibited minimum change in length and orientation during the prenatal period, and thus was used as a reference line. The length of the teeth was calculated from 3D data. The upper first and second molars were longer than the lower ones. When viewed from the upper side, the upper and lower molar primordia were parallel from ED 13.5 to 15.0. During this period, the upper molars had a more lateral position than the lower ones. This situation was maintained in the anterior extremity of the first molars at later stages, while the posterior part of the upper and lower molar epithelia reached opposition in the medio-lateral direction from ED 16.0. The lower incisors exhibited an apparently backward position when compared to the upper incisors at earlier stages. However, the distance between the prospective anterior tips of the opposing incisors gradually decreased. The part of Meckel's cartilage associated with the lower dental quadrant elongated more than 3-fold from ED 13.5 to 18.0, and the lower jaw grew faster than the upper one. This difference resulted from the fast growth of the lower diastema from ED 14.0 to 18.0. The different growth speeds of the upper and lower jaws did not change the relative antero-posterior adjustment of the upper and lower molars, but contributed to achieving the opposition of the gnawing ends of the incisors.