Congenital anomalies, cancer, atrophic vaginitis, and bacterial infections are among the problems to which the vagina is susceptible. The typical microflora present in the human female genital tract differs from that normally found in the tract of the female rat. It has been suggested that this difference is likely related to a difference in vaginal pH (the pH of the rat vagina is higher than that of the human vagina). The main microorganisms present in the rat genital tract include Pasteurella pneumotropica, diphtheroid bacilli, alpha and nonhemolytic streptococci, Proteus mirabilis, and Staphylococcus epidermidis.

In the digital image above, a section of rat vagina tissue is presented that was labeled with the fluorophore Oregon Green 488 conjugated to wheat germ agglutinin, targeting the Golgi network. The sample was also labeled with Alexa Fluor 568 conjugated to phalloidin in order to target filamentous actin and with Hoechst 33342 to counterstain nuclear DNA. Images were recorded in grayscale with a 12-bit digital camera coupled to a Nikon Eclipse 80i microscope equipped with bandpass emission fluorescence filter optical blocks. During the processing stage, individual image channels were pseudocolored with RGB values corresponding to each of the fluorophore emission spectral profiles.