There is a scarcity of studies on the prevalence of Trichomonas vaginalis (TV) in indigenous populations of Brazil. We conducted a cross-sectional study between January and December 2018, on indigenous women living nearby an urban center of the Midwest region of Brazil and determined the prevalence of TV. Factors associated with TV infection and a comparison of molecular and direct microscopy diagnoses were determined. 241 indigenous women aged above 18 years participated in the study. Cervical and vaginal brush samples were collected to diagnose TV through polymerase chain reaction (PCR). Direct microscopy for detection of TV, and cellular changes was performed. A sociodemographic and behavioral questionnaire was applied at the beginning of the study. All the data were analyzed using Statistical Package for the Social Sciences. The result obtained showed that 27.8% [95% CI: 22.2-33.9] were positive for TV on PCR, while 7.41% [95% CI: 4.1-11] showed positive on direct microscopy. Direct microcopy also found 21 (8.71%) and 8 (3.31%) women infected with Gardnerella vaginalis and Candida albicans, respectively. In addition, 10 women presented atypical squamous cells of unknown significance and 14 lesions suggestive of HPV. Single women, under the age of 30 and who do not use condoms, were found to have a greater chance of getting TV infection. The high prevalence TV found in this population is comparable to highly vulnerable populations, as prisoners, sex workers and women in regions with low socioeconomic levels, moreover, seems to be an underdiagnosis of this infection. Therefore, a routine test program, as well as a review of the diagnostic method used, is encouraged for proper management.