Trichomonas vaginalis is an underestimated sexually transmitted infection (STI) associated with numerous clinical sequelae. The true prevalence and clinical impact of trichomoniasis are unknown, as current methods of detection exhibit poor sensitivity compared to molecular amplification methods. Limited data exist comparing the BD Affirm VPIII hybridization assay to the Gen-Probe Aptima T. vaginalis (ATV) transcriptionmediated amplification (TMA) assay for detection of T. vaginalis. In this study, specimens from 766 patients were evaluated. Specimens were retrieved consecutively from patients with vaginal complaints and/or with histories suggestive of STI. Study inclusion was dependent upon the request for and collection of both a vaginal swab for Affirm and a specimen for Aptima Combo 2 by the health care provider during the same office visit. Affirm was performed using the specific collection swab and the transport provided for the test. The ATV assay was performed on remnant Aptima Combo 2 specimens. A second ATV TMA assay, utilizing an alternate T. vaginalis primer and probe set, was performed on all specimens positive by the initial TMA and/or the Affirm assay. Infected-patient status was defined as positive T. vaginalis test results by at least 2 assays. Overall, 5.1% of subjects were positive for T. vaginalis. T. vaginalis was most prevalent in women who were 36 to 45 (11.9%), 51 to 60 (7.7%), and 16 to 25 (4.2%) years of age. The ATV assay was statistically more sensitive than the Affirm assay (100% versus 63.4%, P < 0.0001), identifying 36.6% more positive patients.Despite a worldwide prevalence rate likely to be double that of Neisseria gonorrhea and Chlamydia trachomatis combined, Trichomonas vaginalis is not currently a reportable disease in the United States (1, 7). Recent literature suggests an association between T. vaginalis infection and the sequelae of other sexually transmitted infections (STIs), including low birth weight, premature rupture of membranes, preterm labor, atypical pelvic inflammatory disease, infertility, prolonged carriage of human papillomavirus (HPV), and an increased risk for acquiring HIV (9,10,13,18,21,31,32). Current methods used for the diagnosis of T. vaginalis, including wet mount microscopy, rapid antigen testing, and culture, have been shown to have poor sensitivity compared to molecular amplification methods (6,14,17,19,24,25,27). In addition, variable performance occurs with antigen testing and wet mount microscopy, depending on whether patients are symptomatic or asymptomatic (17, 26). The BD Affirm VPIII (Affirm) assay (Becton Dickinson, Sparks, MD) is the only Food and Drug Administration (FDA)-cleared, direct-specimen, RNA probebased diagnostic test designed to differentiate and identify pathogens associated with bacterial vaginosis (Gardnerella vaginalis) and vaginitis (T. vaginalis and Candida species). The Affirm test is widely used, yet limited data exist comparing this test with other molecular methods (5).The purpose of this study was to evaluate the perf...