The effect of bee pollen Cistus ladaniferus extract on ovariectomy (OVX)-induced bone loss in vivo was investigated. The water-solubilized extracts were obtained from the bee pollen of Cistus ladaniferus. Cistus extract (5.0 or 10.0 mg/100 g body weight) was orally administered once daily for 30 days to OVX rats. The analysis using a peripheral quantitative computed tomography (pQCT) showed that OVX-induced a significant decrease in mineral content, mineral density, and polar strength strain index in the femoral-metaphyseal tissues. These decreases were significantly prevented after the administration of cistus extract (10.0 mg/100 g). Moreover, OVX-induced a significant decrease in calcium content in the femoral-diaphyseal and -metaphyseal tissues. This decrease was significantly prevented after the administration of cistus extract (5.0 or 10.0 mg/100 g). This study demonstrates that cistus extract has a preventive effect on OVX-induced bone loss in vivo.