To investigate the role of the cross-talk between estrogen receptors and peroxisome proliferator-activated receptor gamma in daidzein's prevention and treatment of osteoporosis in the ovariectomized rats. Sixty four-month-old Sprague-Dawley (SD) female rats were divided into six groups. Four weeks after the establishment of osteoporosis model, the ovariectomized rats were administered different drugs by gavage respectively for three months. After sacrificing, the expressions of mRNA of ERalpha, ERbeta and PPARgamma in L(6) and right femur were measured by realtime-RT-PCR, while proteins were detected by immunohistochemistry. The expressions of ERalpha mRNA and protein were significantly lower than that of ERbeta in three dosing groups. Excepting that of rat femur of rats in H-Dai group, the expressions of ERbeta mRNA of lumbar spine and femur in M-Dai group (0.0177 +/- 0.0010, 0.0245 +/- 0.0013) and L-Dai groups (0.0276 +/- 0.0027, 0.0278 +/- 0.0044) and lumbar spine in H-Dai group (0.0163 +/- 0.0037) were significantly higher than that in OVX group (0.0016 +/- 0.0005, 0.0041 +/- 0.0014). There was no significant difference with E(2) group. At the same time, the expression of ERbeta protein showed into the similar trend as that of mRNA. And there was an rising expressions of ERbeta while daidzein dose decreased. On the contrary, the expressions of PPARgamma mRNA and protein decreased. There is an inverse cross-talk relationship between ERbeta and PPARgamma, it may play a role in daidzein's prevention and treatment of osteoporosis in ovariectomized rats.