The objective of this study was to determine the prevalence and concordance of Mycoplasma genitalium (MG) among Mexican American and African American women and their male sexual partners. Secondary objectives were to determine symptoms of MG infection and persistence of MG after antibiotic therapy. Heterosexual couples were tested for MG and interviewed separately regarding symptoms and behavioural/epidemiologic variables at baseline, six and 12 months. The overall prevalence of MG among women and men was 9.5% and 10.6%, respectively. Subjects were five times more likely to be infected with MG if their sexual partner was MG positive. Among men and women, MG prevalence and mean bacterial loads were similar after receiving single-dose azithromycin, doxycycline or no antibiotics. MG was associated with current urethral discharge in men. No clinical symptoms were specifically diagnostic of MG infection in women.