We set out to determine the prevalences of Chlamydia trachomatis and Neisseria gonorrhoeae by ligase chain reaction as well as to determine the prevalence of Trichomonas vaginalis by culture in a large and diverse national sample of non-health-care-seeking young women entering the military; we also sought to compare the abilities of three different techniques of collecting specimens (first-void urine, self-collected vaginal swab, and clinician-collected endocervical swab) to identify a positive specimen. A cross-sectional sample of young women was voluntarily recruited; as a part of their routine entry pelvic examination visit, they completed a self-administered reproductive health questionnaire and provided first-void urine (used to detect C. trachomatis and N. gonorrhoeae) and self-collected vaginal swabs (used to detect C. trachomatis, N. gonorrhoeae, and T. vaginalis). The number of positive tests divided by the number of sexually active women screened by each sampling method determined the rates of prevalence. The rate of infection with any of the three sexually transmitted diseases (STDs) tested was 14.1%. The total positive rates for each STD (identified by ≥1 specimen) were the following: for C. trachomatis, 11.6%; N. gonorrhoeae, 2.4%; and T. vaginalis, 1.7%. The proportions of positives identified by specimen type were, for C. trachomatis and N. gonorrhoeae, respectively, endocervix, 65 and 40%; urine, 72 and 24%; and vagina, 81 and 72%. The proportions of positives when specimen results were combined were, for C. trachomatis and N. gonorrhoeae, respectively, cervix plus urine, 86 and 49%; cervix plus vagina, 91 and 93%; and vagina plus urine, 94 and 79%. We concluded that STDs were epidemic in this population. Self-collected vaginal swabs identified the highest number of positive test results among single specimens, with the combined cervix-vagina results identifying the highest number of positive results. Self-collected vaginal swab collections are a feasible alternative to cervical specimen collections in this population, and the use of multiple types of specimens increases the positive yield markedly.