Introduction: Sexually transmitted infections (STIs) disproportionately affect transgender women, who often lack access to healthcare due to stigma and discrimination. In Brazil, there is limited data on the prevalence of HIV, syphilis, viral hepatitis, and other STIs. This DrPH study aimed to detail the clinical epidemiology of Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), and human papillomavirus (HPV) among transgender women in Brazil to better inform approaches for the control of STIs. Methods: TransOdara was a multi-centric, cross-sectional STI prevalence study conducted in five capital cities representing all Brazilian regions, between December 2019 and July 2021. A total of 1,317 transgender women aged >18 years were recruited using respondent driven sampling, completed an interviewer-led questionnaire, offered a physical examination, and provided samples from multiple sites (anorectal, oropharyngeal, and urogenital) to detect Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and human papillomavirus (HPV). Data analysis determined the uptake of physical examination, acceptability of sample collection methods, and comparability of self-sampling to provider-collection for the detection of STIs by transgender women in Brazil. Results: This study found a high prevalence of anorectal NG (9.1%) and CT (8.9%) infections, with most being asymptomatic (87.6% and 88.9%, respectively). Anorectal prevalence of high-risk HPV types was also high (66.2%). Most participants consented to a general examination (65.4%), but less than half permitted a genital (42.3%) or anal (42.1%) examination. With regards to preferred sample collection for STI testing, most selected self-collection for anorectal (74.9%) and genital (72.7%) samples. Test positivity rates from self-collection were comparable to provider-collected samples. Conclusion: This study highlights the need to integrate periodic multi-site NG/CT screening into sexual health services offered to transgender women, due to the high prevalence of asymptomatic infections. While molecular NG/CT testing should guide treatment for symptomatic cases, syndromic management suits resource-constrained settings due to high cost and limited diagnostic capacity, compounded by the absence of affordable point-of-care (POC) tests. For both STI screening and testing, offering the option of self-collected samples is essential. Self-sampling was found to be well-accepted and yielded comparable results to provider-collected samples. The study concludes that the choice of collection methods supports gender-affirmative care and has the potential to enhance accessibility of sexual health services for transgender women.