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To quantify sexual orientation and gender identity (SOGI) disparities in incidence of HIV, other sexually transmitted infections (STIs), and viral hepatitis.We performed a records-based study of 19 933 patients visiting a federally qualified health center in Los Angeles, California, between November 2016 and October 2017 that examined HIV, STIs, and viral hepatitis incidence proportions. We created multivariable logistic regression models to examine the association between incidence proportions and SOGI among people living with HIV and HIV-negative patients.Among those who were HIV-negative at baseline (n = 16 757), 29% tested positive for any STI during the study period, compared with 38% of people living with HIV. Stratified by birth sex, STI positivity was 32% among men and 11% among women. By SOGI, STI positivity was 35% among gay and bisexual cisgender men, 15% among heterosexual cisgender men, 11% among cisgender women, 25% among transgender women, 13% among gay and bisexual transgender men, 3% among heterosexual transgender men, and 26% among nonbinary people.Stratifying by SOGI highlighted disparities that are obscured when stratifying by birth sex.To monitor and reduce disparities, health jurisdictions should include SOGI data with infectious disease reporting.