Herba Epimedii, Fructus Ligustri Lucidi and Fructus Psoraleae are three frequently used Chinese herbs traditionally used for tonifying the 'kidney system'. They were selected for the present study to formulate an herbal preparation with a weight ratio of 5:4:1 based on their phytochemical, nature, documented treatment efficacy and toxicity. The dosing effects (1 g/day, 0.5 g/day and 0.175 g/day) of the antiosteoporosis function of the water extract of this formula were tested in ovariectomy- and calcium deficiency-induced osteoporotic rats. Eleven weeks of herbal treatment demonstrated a beneficial effect on the preservation of bone mineral density (BMD) at the femur neck in a dose-dependent manner with the preference for higher dosage. No significant increase in uterus weight was observed in the herbal formula treated rats. In addition, microarray data of kidney tissue revealed that this herbal formula was able to down-regulate the expression of phase II drug metabolizing enzymes, similar to the effects of estrogens.