The effects of long-term, artificially created, hypofunctional occlusion and its recovery on the morphology of the first molar root in mice have been investigated. C57BL/6J (Jackson Laboratory, Bar Harbor ME, USA) mice were randomly divided according to their periodontal conditions into normal, hypofunctional, and recovery groups (n = 4). In the experimental hypofunctional and recovery groups, a bite-raising appliance was set to produce hypofunction at the molar region. All groups were analyzed at 16 weeks of age using a light microscope. Root length, width, and area as well as the thickness and the area of the periodontal ligament (PDL) space of the maxillary first molar were calculated. Roots were longer and narrower in the hypofunctional group than in the control group. The mesial root in particular was markedly affected. Root area was significantly smaller in the hypofunctional group than in the other groups. PDL thickness and area were also significantly less in the hypofunctional group than in the control group, but were greater in the recovery group than in the hypofunctional group. These results suggest that root size and the PDL structure may be reduced by disuse atrophy resulting from a defect in occlusal function, but may be recovered following the gain of occlusal stimuli.