Background: Ovarian function and morphology of owl monkeys (Aotus spp.) is inadequately known, but it is essential to describe this organ in detail to better understand reproductive patterns of the species. Methods: This study reports the anatomical and histological features of the ovaries from 41 owl monkeys, considering their reproductive status and parity. Results: The corpora lutea (CL) and reproductive state had a significant effect on ovarian volume. Follicles were observed in both pregnant and non-pregnant subjects. All females in the luteal phase and pregnant females showed at least one cyclic or pregnancy CL. Mean ovulation rate was 1.89 CL/female, and the mean ovum mortality was 37.5%. There were no significant differences in ovarian volume related to parity. Conclusions: These results contribute to the scarce information available on the reproductive biology of owl monkeys and can aid in the development of biotechnologies involved in assisted reproduction.