The aim of this study was to evaluate the rat ovarian morphological and function changes after pinealectomy (px). Two months after px, young female Wistar rats were sacrificed and the right ovaries were analysed morphologically and the left ovaries were used for steroid receptor binding experiments. Blood was collected and steroid hormone and melatonin levels were measured using radioimmunoassay kits. Results revealed that in the px group the rat ovaries had an increase in the number of atretic follicles and interstitial cells. These cells showed hyperactivity features on transmission electron microscopy and morphometric analysis (p < 0.05 compared with control and sham groups). Px-group serum showed an increase in estradiol (p < 0.05) and a decrease in progesterone levels (p < 0.05) compared with other groups. Moreover, progesterone receptor expression was lower than control and sham groups (p < 0.05). We postulate that pinealectomy leads to many morphological alterations of rat ovaries that are associated with functional changes in steroidogenesis and a decrease in progesterone receptor expression.