The aim of this study was to determine the short-, mid- and long-term effects of cloprostenol (a synthetic analogue of prostoglandin F2 alpha, PG) and equine chorionic gonadotropin (E) administration on reproductive organs (uterine tissue and ovaries) in female rats. Three different groups, PG, E, and control (C), were created, as well as six subgroups of the PG and E groups. After the treatment procedure, reproductive organs were removed surgically 7, 14, and 21 days after the last injection. Morphometric and histopathological changes in tissues were evaluated. It was shown that PG and E had a moderate proliferative effect on epithelial cells and endometrial glands, especially in the mid-term. It was also observed that, regardless of the time of application, some pathological changes can result from hormone administration.