Population surveys involving the monitoring of high-risk sexual behavior have been recognized as important public health tools to control the HIV epidemic and other sexually transmitted infections (STIs). Using data from the Knowledge, Attitudes, and Practices survey (PCAP-2013) and from the National Health Survey (PNS), indicators of sexual behavior were compared according to sociodemographic characteristics, including size (%) estimates of men who have sex with men (MSM) and women who have sex with women (WSW). To compare PCAP and PNS proportional distributions, the Pearson's chi-square test, adjusted by the Rao-Scott’s correction, was applied. Using data from the PNS-2019, experience of violence (verbal, physical, and sexual) was analyzed according to sexual orientation. Odds ratios (OR) were estimated by logistic regression models using each type of violence as the response variable and sexual orientation (heterosexual, homosexual/bisexual) as the independent variable. Size (%) estimates of MSM and WSW, obtained by direct questions from the PCAP-2013, showed lower homosexuality prevalence estimates than those resulting from the PNS-2019 self-declared sexual orientation. Significant differences were found between the MSM proportions according to the PCAP-2013 (3.7%; 95% CI 3.1–4.4%) and to the PNS-2019 (2.2%; 95% CI 1.9–2.5), and between the WSW proportions (4.6%; 95% CI 4.0-5.4%) and (2.1%; 95% CI 1.8–2.4), respectively. Regarding condom use at last sexual intercourse, no differences between the PCAP-2013 and the PNS-2019 estimates were found at the national level, but significant improvements were found for MSM, people aged 18–24 and 25–34 years, and individuals not living with a partner. Violence-related indicators showed that over 40% of homosexual/bisexual men and women have suffered some type of violence in the past 12 months. Regarding sexual violence, at least once in a lifetime, prevalence was 18.1% among MSM, with 10-fold greater odds (9.9; 95% CI 6.7–14.8) than that of heterosexual men. Among WSW, prevalence was 25.6%, with an estimated OR of 3.3 (95% CI 2.4–4.3). The findings emphasize the importance of monitoring HIV/STI risk-related practices and violence experienced by sexual minorities at subnational levels in order to strengthen public policies focused on overcoming the persistent homophobic prejudice in the Brazilian society.