Background Data on testing rates and prevalence of and factors associated with genital and extragenital chlamydia and gonorrhea among transgender women with HIV in the United States are limited. Methods This retrospective cohort analysis included transgender women living with HIV enrolled in the US Centers for AIDS Research Network of Integrated Clinical Systems cohort between January 2005 and December 2016 with chlamydia or gonorrhea testing performed in HIV clinic. The primary outcome was a positive test result for chlamydia or gonorrhea at urogenital or extragenital (rectal/pharyngeal) sites. Factors associated with infection were examined using logistic regression and generalized estimating equations to account for multiple tests per woman. Results Among 312 transgender women in HIV care, 252 (81%) were tested for chlamydia or gonorrhea at least once. Annual testing rates were low: 23% to 53% at genital sites and 24% to 47% at extragenital sites. A total of 88 infections were detected, and 22% of women (55/252) had at least one positive test result. Most infections occurred at extragenital sites (80% of chlamydia and 82% of gonorrhea positive test results). Factors associated with infection in an adjusted model were as follows: age 18 to 29 years compared with =50 years (adjusted odds ratio [aOR], 7.6; 95% confidence interval [CI], 1.8-31.2), CD4 count >350 compared with CD4 <200 (aOR, 5.5; 95% CI, 1.2-25.1), and higher engagement in HIV care (aOR, 2.2; 95% CI, 1.0-4.5). Conclusions Among transgender women living with HIV, testing rates for chlamydia and gonorrhea are inadequate, particularly at extragenital sites where most infections occur.