Thirty-three women with histologically confirmed cervical intraepithelial neoplasia (grades I to III, with one case of microinvasive carcinoma) and 54 women without evidence of the disease were prospectively studied to determine the relationship of genital infection to cervical neoplasia. Demographic and sexual data for patients and control subjects were collected, with standardized clinical and colposcopic evaluation by means of predefined diagnostic categories. Cultures from the cervix were examined for herpes simplex virus, cytomegalovirus, Chlamydia trachomatis, and Neisseria gonorrhoeae. Human papilloma virus infection was identified by characteristic changes of koilocytosis in cytologic or histopathologic specimen. Cultures from the vagina were evaluated for Gardnerella vaginalis, Trichomonas vaginalis, Ureaplasma urealyticum, Mycoplasma hominis, Candida albicans, and other yeasts. Separate Gram strains were prepared from endocervical secretions and from vaginal secretions. More lifetime sexual partners, larger area of transformation zone, evidence of human papilloma virus infection, and altered vaginal flora were observed in women with cervical intraepithelial neoplasia. The association of human papilloma virus infection and altered vaginal flora with cervical intraepithelial neoplasia was independent of sexual experience.