Functional morphology may provide important information that could improve methodologies for the diagnosis of the reproductive phase of females, and develop assisted breeding techniques for wildlife. This study examined features of genital organs in 19 Peruvian red uakari monkey (Cacajao calvus ucayalii) females in different reproductive stages, collected from wild animals hunted for food by rural communities in the North-eastern Peruvian Amazon, in order to provide knowledge on the reproductive physiology of this species. The observed mean ovulation rate was 1.4 follicles, and the observed maximal follicle diameter was 0.8 cm. After ovulation, the matured follicle luteinizes resulting in functional CL. In case of oocyte fertilization, the pregnancy CL grows to a maximum of 1.2 cm in diameter, and luteal volume per female decreases related to the advance of pregnancy. Pregnant females also present follicular activity until late pregnancy, but non-ovulated follicles do not undergo atretic processes and apparently transform to accessory CL, resulting in a contribution of 30% of the total luteal volume. All pregnant females delivered a single fetus at term, resulting in a rate of reproductive wastage of 20% of oocytes or embryos. The endometrium and the endometrial glands in non-pregnant females in the follicular phase show a significant increase related to the follicular growth, reaching a high proliferation in non-pregnant females in the luteal phase. The red uakari monkey showed different vaginal epithelium features in accordance with the reproductive state of the female, suggesting that vaginal cytology could be a successful methodology with which to characterize the estrous cycle of this species. The present reproductive evaluation of the Peruvian red uakari monkey provides important information that could improve the development of assisted reproductive techniques in non-human primates. Am. J. Primatol. 75:545-554, 2013. © 2013 Wiley Periodicals, Inc.