Trichomonas vaginalis infections are usually asymptomatic or can result in non-specific clinical symptoms, which makes laboratory-based detection of this protozoan parasite essential for diagnosis and treatment. We report the development of a battery of highly sensitive and specific PCR assays for detection of T. vaginalis in urine, a non-invasive specimen, and development of a protocol for differentiating among Trichomonas species that commonly infect humans.