We estimated the prevalence of syphilis and (CT) and (NG) infections, as well as human immunodeficiency virus (HIV) coinfection among cisgender men who have sex with cisgender men (MSM) and transgender women (TW) in Tijuana, Mexico. MSM and TW ( = 212) recruited via respondent-driven and venue-based sampling for HIV testing underwent sexually transmitted infection (STI) testing and completed interviewer-administered surveys in this study (2017-2018). Treponemal rapid tests were used at the point-of-care with positives undergoing confirmatory testing following the reverse syphilis-testing algorithm. Nucleic acid amplification testing of urine and swabs (rectal and pharyngeal) was used to detect CT/NG at three anatomic sites. Chi-squared tests were used to compare STI prevalence by HIV status. Sexually transmitted infection prevalence was 39.6% overall but higher for newly diagnosed HIV-positive (55.7%; = 88) than HIV-negative (28.2%; = 124) participants (-value < 0.0001). Among newly diagnosed HIV-positive participants, the prevalence of syphilis was 35.2% (31/88), CT infection was 27.3% (24/88; nine urethral; 16 rectal; four pharyngeal), and NG infection was 26.1% (23/88; six urethral; 19 rectal; nine pharyngeal). Among HIV-negative participants, the prevalence of syphilis was 12.1% (15/124), CT infection was 13.7% (17/124; seven urethral; nine rectal; two pharyngeal), and NG infection was 9.7% (12/124; three urethral; seven rectal; seven pharyngeal). Over 60% of all CT (25/41) and NG (26/35) infections in the full sample occurred extragenitally in the absence of urethral infections, and over 80% of rectal (30/37) and pharyngeal (16/18) infections were asymptomatic. The high prevalence of syphilis, CT, and NG infections among MSM and TW in Tijuana suggests STI screening that includes extragenital tests, particularly at HIV diagnosis, may help curb HIV/STI transmission.