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There are high rates of Trichomonas vaginalis in remote areas of Central Australia. Conventional tests for T. vaginalis have low sensitivity in this setting. Aims of the study were to estimate the prevalence of T. vaginalis, to assess the presence of clinical signs and symptoms, to compare a T. vaginalis polymerase chain reaction (PCR) test with conventional methods of diagnosis, and to compare the PCR from different samples, including self-collected swabs (SCS). Of 205 women recruited, the prevalence of T. vaginalis was 24%. The prevalence of T. vaginalis was higher in women under 25 years (33%), compared with those who were 25–34 years (26%) and those over 35 years (15%, P< 0.05). The sensitivity of T. vaginalis PCR detection from SCS (94%) was not statistically different from a practitioner-collected HVS (96%), but was superior to urine PCR (74%) and conventional methods. After multivariate analysis, those women with high pH were almost three times more likely to be positive for T. vaginalis (odds ratio=2.71 with 95% confidence interval 1.06–6.93, P=0.037). Superior assays such as PCR should be a diagnostic option to adequately screen and treat women with T. vaginalis, in order to reduce complications, including the increased risk of HIV transmission.