We evaluated the effects of YM529, a nitrogen-containing bisphosphonate, on the repair of cortical bone after drill-hole injury at the tissue-, cell- and gene-levels in the femur of mice. Eight-week-old male C57BL/6N mice were treated with an intravenous injection of 0.01, 0.05 and 0.1 mg/kg body weight (BW) of YM529, or the vehicle (VC) once a week from 8 weeks of age until sacrifice. At 10 weeks of age (day 0), a drill-hole was made in the diaphysis of bilateral femurs. Femoral specimens were obtained at days 3, 5, 7, 10, 14, 21 and 28 after surgery. Histology and histomorphometry confirmed the early woven bone formation in 7 days after injury in all four groups, but the following lamellar bone repair in the cortical tissue area delayed only in the YM529-treated groups. Since the findings were not dose-dependent, following evaluations were performed in VC and YM529 0.1 mg/kg BW dose groups. Calcein-labeled surface of regenerated bone decreased at day 21 in the YM529 group. At day 0, CFU-f number and mineralized nodule area that developed from marrow cells were significantly smaller in YM529 group than in VC group. At day 5, however, these values increased to levels similar to those in VC group. The mRNA expression levels of BMP-2, cbfa1, osterix, type I collagen, and osteocalcin in the injured bone and marrow cells at days 3 and 5 were similar in the two groups, but were higher in YM529 group at day 7 compared with that in the VC group. At day 14, the levels of these mRNAs were still high, while that of osteocalcin was significantly reduced compared to the VC group. These data indicate that the action of YM529 on bone formation is bimodal, stimulatory on the developments of osteogenic cells for the woven bone regeneration and inhibitory on the terminal differentiation of osteoblasts for the later remodeling, consequently leading to a delay in the lamellar bone healing in the cortical tissue area.