Masticatory functional changes have been shown to influence the quantity and quality of the alveolar bone during growth. This study was designed to investigate the effect of masticatory function rehabilitation on the morphology and the trabecular architecture of the mandibular alveolar bone after cessation of growth. Forty-four Sprague-Dawley male rats received soft diet in order to develop masticatory muscle hypofunction. After 21 weeks, after cessation of growth, the animals were divided into two groups: the first group continued receiving soft diet for six more weeks (hypofunction group), while the second group changed to ordinary (hard) diet with the aim to restore a normal masticatory function (rehabilitation group). A third group of 16 male rats (normal group) received ordinary (hard) diet during the whole experimental period and served as control. Micro-tomographic histomorphometry was used to evaluate the architecture of the mandibular alveolar bone (e.g. bone volume fraction, trabecular thickness, trabecular separation, etc.) at the end of the experiment (27 weeks). The height and width of the alveolar process were measured as well. The alveolar process trabecular bone volume fraction (BV/TV) was lower for the animals of the hypofunctional group as compared to those of the normal (p<0.01) and the rehabilitation (p<0.05) groups. Despite the significant improvement observed in the rehabilitation group, their BV/TV was lower in comparison to the normal group (p<0.05) at the end of this experiment. All the other micro-tomographic parameters followed the same pattern of change between groups; values of the rehabilitation group were between the values of the two other groups, differing significantly from both of them. The alveolar process was significantly shorter in the normal group in comparison to both the hypofunctional and rehabilitation groups (p<0.05). On the other hand, both the normal and rehabilitation groups were had a wider alveolar process than the hypofunctional group (p<0.05). Both alveolar height and width were significantly correlated with all micro-tomographic parameters under study. The rehabilitation of masticatory function led to a significant improvement of alveolar bone architecture in adult rats, although the negative effects of hypofunction were not totally reversed during the period under study.