The prevalence of selected microorganisms in the lower genital tract in postmenarchal adolescent girls was assessed, including vaginal Gardnerella vaginalis, group B streptococcus, lactobacillus, Mycoplasma species, Ureaplasma urealyticum, Staphylococcus aureus, and yeast, and endocervical Mycoplasma species, U. urealyticum, Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis. Specific attention was focused on important sexually transmitted disease organisms, and differences in isolations by age, sexual activity, ethnicity, contraception, and the diagnosis of nonspecific vaginitis were measured. Sexually active subjects had a mean of 6.05 organisms (SD = 3.16), compared with 3.12 organisms (SD = 3.92) in non-sexually active subjects (P = 0.001). Sexually active subjects had significantly more vaginal G. vaginalis, lactobacilli, Mycoplasma species, and U. urealyticum, as well as endocervical Mycoplasma species and U. urealyticum, compared with non-sexually active subjects; C. trachomatis, N. gonorrhoea, and T. vaginalis were isolated exclusively from the sexually active group. Significant differences in isolation rates by ethnicity were found in vaginal Mycoplasma species and U. urealyticum, and endocervical Mycoplasma species, U. urealyticum, C. trachomatis, N. gonorrhoeae, and T. vaginalis. In general, organisms were isolated from blacks most frequently; N. gonorrhoea was isolated from blacks exclusively. Differences were found in microbiologic isolations by the presence or absence of nonspecific vaginitis. Vaginal G. vaginalis and Mycoplasma species and endocervical Mycoplasma species and U. urealyticum were found significantly more often in isolates from the group with nonspecific vaginitis. It is important to define the microbial flora of the lower genital tract in adolescent girls in order to understand its role in the pathogenesis of acute salpingitis.