Functional morphology of the reproductive organs is a key component for the better understanding of reproductive patterns as well to maximize reproductive efficiency and to develop assisted breeding techniques adapted to wildlife. This study examined anatomical and histological characteristics of genital organs of 60 Poeppig's woolly monkey females in the wild in different reproductive stages, collected by rural hunters in the northeastern Peruvian Amazon. The endometrium, the endometrial glands, and the myometrium showed a significant increase in size related to the follicular growth. In nonpregnant females in the follicular phase, the endometrium, the endometrial glands, and the myometrium showed a significant increase related to the follicular growth. Nonpregnant females in the luteal phase had a thicker endometrium, a greater proliferation of endometrial glands, and a thicker myometrium, compared to females in the follicular phase. Nonpregnant females with small antral follicles presented high amounts of collagen beneath the endometrial epithelium, a sign of endometrial regeneration after menstruation that could be useful for the diagnosis of the reproductive phase in this species. A larger proportion of secreting cervical glands was observed in pregnant females compared to other females. The cervical mucous secretion occupied the lumen of the endocervical canal, assuring that no material could enter the uterus during gestation. The Poeppig's woolly 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 wild primates. The present reproductive evaluation of Poeppig's woolly monkey provides important information that could improve the methodologies for the diagnosis of the reproductive phase of females, the assisted reproductive techniques in non-human primates, and could also give us opportunity for comparative studies and an insight into the evolution of animal reproductive biology, including humans. Am. J. Primatol. 74:1006-1016, 2012. © 2012 Wiley Periodicals, Inc.