The development of the mandibular condylar cartilage is important for the overall growth of the mandible. However, there have been a few researches into medical approaches aimed at controlling condylar growth. This study examined the effects of bisphosphonate on the growth of the condylar cartilage. Alendronate (3.5 mg/kg/week) was administered to postnatal day 1 SD rats for 7 and 10 days. The thickness of each chondrocyte layer and the level of MMP-9 expression were measured. The anteroposterior diameter of the developing condyle was unaffected by the alendronate treatment for 7 days (P > 0.05). The total thickness of the cartilage layers was also unaffected by the treatment for 7 days (P > 0.05). In particular, there was no change in the thickness of the perichondrium and reserve cell layer at the measured condylar regions (P > 0.05). However, the thickness of the proliferating cell layer was reduced significantly, whereas the thickness of hypertrophied cartilage layer was increased (P < 0.05). The number of chondroclasts engaged in hypertrophied cartilage resorption was reduced significantly by the alendronate treatment (P < 0.05). The level of MMP-9 expression was reduced at both the transcription and translation levels by the alendronate treatment for 7 and 10 days. These results indicate that alendronate (>3.5 mg/kg/week) inhibits the longitudinal growth of the mandibular condyle by inhibiting chondrocyte proliferation and the resorption of hypertrophied cartilage for ossification.