The skeletal anchorage system (SAS) was developed to provide intraoral absolute anchorage for the intrusion or distalization of molars. The purpose of this study was to verify the effects of remarkable molar intrusion on the tooth root and the maxillary sinus floor. Six adult female beagles with fully erupted dentition were used. Titanium miniplates were implanted bilaterally above the maxillary second premolar root apices using pentobarbital anesthesia. The second premolars were intruded for four or seven months after three months of healing after implantation. Standardized dental radiographs were taken periodically to evaluate the amount of tooth movement and root resorption. After the experimental animals were fixed by perfusion at the end of each experimental period, the second premolars were dissected along with the surrounding alveolar bone. Undecalcified (60 microm thick) and decalcified (five microm thick) sections were prepared. The average extent of intrusion was 1.8 mm after four months and 4.2 mm after seven months. The root apices of the intruded molars penetrated into the nasal cavity. Remodeled bone around the intruded molar toots was rich in woven bone on the buccal side, whereas that on the palatal side was rich in lamellar bone. Nasal floor membrane and a thin layer of newly formed bone, which lifted intranasally, covered the intruded molar root. Root resorption partly reached into the dentine without the formation of reparative cementum, and little or no serious pathological changes were seen in the pulp of the intruded molars. SAS effectively intruded maxillary molars, but some moderate root resorption was observed.