In this study, we investigated the morphometric and histological alterations of the ovary and uterine horns in 4-week-old rats that were prenatally exposed to diclofenac sodium (DS). For this purpose, pregnant rats were divided into two groups: the control and drug-treated groups. Beginning from the 5th day after mating through the 15th day of pregnancy, DS (1 mg/kg daily) was intraperitoneally injected in the treated group. No injection was given to the rats in the control group. After spontaneous delivery, male off spring were obtained. At the end of the 4th week, ovary and uterine horn samples were removed. Following dissection and routine histological preparation, histopathological and stereological investigations were carried out. Our results indicate that DS application leads to a decrease in the mean volume fraction of the uterine horn. Moreover, there was an increased volume fraction in some structures of the ovary; like the cortex, medulla and zona granulosa. There was no difference found between the two groups in terms of the mean volume of the antrum and the Graafian follicle fraction. Finally, in light of our findings, we may suggest that DS may lead to adverse effects in rats that are prenatally subjected to this drug.