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In the United States, a context of multiple marginalization shapes sexual health disparities experienced by transgender women. Using data from 396 transgender women with negative or unknown HIV status, we performed exploratory factor analysis on responses to gender identity and sexual behavior stigma items and regressed sexual health outcomes on extracted factors via modified Poisson regression with robust variance estimation. Overall, 97.2% of participants endorsed ≥ 1 gender identity stigma; 67.2% endorsed ≥ 1 sexual behavior stigma; and 66.9% endorsed ≥ 1 of each. Extracted factors included gender-identity social stigma, reflecting experiences related to family, fearfulness in public, and verbal harassment (α = 0.68); gender-identity institutional stigma/violence, reflecting experiences related to healthcare, police interactions, and interpersonal violence (α = 0.73); and global sexual behavior stigma, reflecting experiences related to family, friends, and healthcare, as well as police interactions, fearfulness in public, verbal harassment, and interpersonal violence (α = 0.83). Gender-identity social stigma was significantly, positively associated with testing for HIV and testing for sexually transmitted infections. Gender-identity institutional stigma/violence and global sexual behavior stigma were both significantly, positively associated with condomless anal sex, sex work, testing for HIV, testing for sexually transmitted infections, and use of HIV pre-exposure prophylaxis. Stigma-mitigation remains critical to improve quality of life and sexual health for transgender women in the United States.