Objective: To analyze the effects of subchronic cypermethrin on the ovary and endometrium as well as the involvement of apoptosis in the toxicity of cypermethrin. Methods: A total of 32 female Wistar rats were randomly divided into four groups, with 8 rats in each group. The control group received no treatment, and the other three groups received oral cypermethrin at 10, 15 or 20 mg/kg body weight for 28 days (sub-chronic). The granulosa cells were calculated histopathologically. The apoptotic index was determined by in situ technique. Histopathological examination was performed on the uterus and ovary. Results: There was no significant difference in the number of primary follicular granulosa cells between the treatment groups and the control group (P>0.05). However, the number of secondary and tertiary follicle granulosa cells in the treatment groups was significantly decreased compared to that of the control group (P all<0.05). The apoptotic index of primary follicular granulosa cells increased significantly in the groups treated with cypermethrin compared with the control group (P<0.05). The secondary, tertiary, and endometrial granulosa cell apoptosis index was significantly higher in all treatment groups compared to the control group (P<0.05). The higher the dose of cypermethrin was, the higher the apoptotic index of secondary, tertiary and endometrial granulosa cells was. There was a significant decrease in endometrial thickness in the three treatment groups compared to the control group (P<0.05). Thinning of the endometrial layer was seen in the cypermethrin exposure groups. Conclusions: Exposure to cypermethrin can suppress the number of secondary and tertiary follicular granulosa cells, and trigger thinning of the endometrium through induction of apoptosis.