Background: A baboon, a non-human primate, is phylogenetically close to human and has been used to study in detail aspects of reproductive physiology that cannot be studied in humans for ethical reasons. Objective: To determine the histological changes in baboon vagina associated with cyclic variations during normal menstrual cycle. Setting: The experiments were carried out at Institute of Primate Research (IPR), Karen, Nairobi, Kenya. Subjects: Nine adult healthy female olive baboons were used in this study. These baboons were monitored over a period of one year and found to have regular menstrual cycles. The vaginal biopsies were taken at different menstrual stages, fixed in 10% formalin and processed to evaluate histological changes. Results: Observation of the histological sections of the biopsies by light microscopy showed that there were histological changes associated with cyclic variations in female olive baboon. During the luteal phase, menstrual phase and pregnancy the squamous epithelium was very thin. The layer gradually thickens throughout the proliferative phase and was thickest during the ovulation period. Conclusion: The changes in squamous epithelium suggest that the baboon vagina undergoes histological changes throughout the menstrual cycle which may be associated with hormonal variations. The data from this study also suggest that olive baboon is a good model for investigating possible effects of hormonal contraceptives on vaginal epithelium and the mechanism of female heterosexual transmission of HIV.