Exposure of female rats to continuous light for prolonged periods induces persistent estrus (PE), an anovulatory disorder. Instead of cyclic fluctuations, the vaginal smears from PE rats show only cornified cells as the hormonal control of the estrous cycle becomes inappropriate, and ovaries become cystic when ovulation ceases. The reproductive tract, a key target organ in PE, shows numerous manifestations of chronic estrogenic influence.In this paper, we report our findings on bacterial colonizations and ultrastructural examinations of the vaginal surface epithelium of PE rats with polycystic ovaries (PCO). Quantitation of bacteria in the vaginal lavage was done with a standard volume of sterile normal saline and studied in five different hormonal states: diestrus day 1 (D-1), diestrus day 2 (D2), proestrus (Pro E), estrus (E), and persistent estrus (PE). Scanning electron microscopy (SEM) was used to examine the vaginal surface epithelium from PE rats with PCO and compared to the controls. In all rats, cardiovascular perfusion was performed for in vivo fixation of the organs using 2.5% glutaraldehyde in 0.1 M Na Cacodylate buffer (pH 7.3) for 30 minutes.