The presence of sexually transmitted pathogens in the vagina of the sexually abused girl may provide direct evidence of sexual abuse; the presence of other abnormal vaginal organisms may provide indirect evidence of abuse. To identify abnormal vaginal organisms, we prospectively studied the flora of 209 sexually abused girls (cases) and compared it with that in a concurrent control group of 108 girls. Case and control subjects were from the same community, were predominantly white, and 71% of each group were 3 to 10 years of age. The sexually transmitted pathogens (Neisseria gonorrhoeae, Trichomonas vaginalis, Chlamydia trachomatis, herpes simplex virus) were isolated exclusively from the case group at a low frequency (less than 1%). The isolation of Mycoplasma species exclusively in the case group (4%), and of Gardnerella vaginalis in 7% of the case group versus 1% of the control group, suggests that both these organisms may be sexually transmitted. Other bacteria also were collectively more frequent in the case group (16% vs 6%). There may be an association between sexual activity and colonization of the lower genital tract in young girls.