Background Estrogen deficiency causes atrophic changes within the urogenital tract, and is associated with urinary symptoms. The purpose of this study was to investigate the effects of estrogen and tibolone on bladder histology, and the changes of estrogen receptor alpha and beta(ER alpha and beta) protein expression in the detrusor muscle. Methods Forty female rats were separated into four groups of ten each. They received a sham operation (Sham), ovariectomy (Ovx), ovariectomy plus estrogen replacement (Ovx+E), or ovariectomy plus tibolone treatment (Ovx+T). After 12 weeks each rat was anesthetized and the bladders were removed. The bladders' ultra structure, collagen fiber (CF) to smooth muscle(SM) ratio and ER subtypes were studied. Statistical analyses were performed using the one-way analysis of variance test. Results Ovx resulted in significant degeneration in bladder ultra structure; however, estrogen and tibolone reversed those changes. Ovx increased the CF/SM ratio, estrogen and tibolone resulted in an increase. Two estrogen receptors (ERs) were expressed in the bladder detrusor, with ER beta the main subtype. Ovx resulted in up-regulation of ER alpha and down-regulation of ER beta. With estrogen and tibolone treatment, ER beta showed a significant increase but ER alpha showed no significant difference compared with Ovx. Conclusions Estrogen deficiency deteriorates bladder ultra structure and histology. Supplementary estrogen can improve bladder function which may be due to inhibition of collagen hyperplasia and increased SM density. ER beta has an important role in mediating estrogen function in the bladder. Tibolone has a mild estrogenic action and has an effect on bladder function and structure to some degree.