Few comparative data are available internationally to examine health differences by transgender identity. A barrier to monitoring the health and well-being of transgender people is the lack of inclusion of measures to assess natal sex/gender identity status in surveys. Data were from a cross-sectional anonymous online survey of members (n > 36,000) of a sexual networking website targeting men who have sex with men in Spanish- and Portuguese-speaking countries/territories in Latin America/the Caribbean, Portugal, and Spain. Natal sex/gender identity status was assessed using a two-step method (Step 1: assigned birth sex, Step 2: current gender identity). Male-to-female (MTF) and female-to-male (FTM) participants were compared to non-transgender males in age-adjusted regression models on socioeconomic status (SES) (education, income, sex work), masculine gender conformity, psychological health and well-being (lifetime suicidality, past-week depressive distress, positive self-worth, general self-rated health, gender related stressors), and sexual health (HIV-infection, past-year STIs, past-3 month unprotected anal or vaginal sex). The two-step method identified 190 transgender participants (0.54%; 158 MTF, 32 FTM). Of the 12 health-related variables, six showed significant differences between the three groups: SES, masculine gender conformity, lifetime suicidality, depressive distress, positive self-worth, and past-year genital herpes. A two-step approach is recommended for health surveillance efforts to assess natal sex/gender identity status. Cognitive testing to formally validate assigned birth sex and current gender identity survey items in Spanish and Portuguese is encouraged.