The aim of this study was to examine histomorphologically how bisphosphonate (BP) injected before and after implant placement surgery affects the peri-implant bone in vitamin D-deficient animal model. This study used 60 six-week-old male Sprague-Dawley (SD) rats which were given a vitamin D-deficient diet. These experimental animals were divided into Group 1 (BP administration starting before implant placement), Group 2 (control group) and Group 3 (BP administration starting after implant placement). Threaded titanium implant was placed 0.50 mm mesial to the first molar. The samples were tissues from Groups 1 and 2 obtained at 1, 2, 4 and 8 weeks after implant placement and tissues from Group 3 obtained after the start of BP administration. Evaluation by light microscope and micro-CT imaging were performed. In Group 1, bone density around implants significantly increased as time progressed from after implant placement. In Group 3, bone density significantly decreased as the duration of bisphosphonate use increased. Group 1 had a significantly higher proportion of lacunae without osteocytes compared with Group 2 after implant placement. In Group 3, the proportion of these lacunae increased significantly from one to two weeks after the start of bisphosphonate administration. There were significantly higher proportions at 4 weeks and 8 weeks after the start of administration compared with 1 week after the start. This histological result suggests the need to exercise caution in using implant treatment on patients taking bisphosphonates and in administering bisphosphonates in patients after implant placement.