India has one of the largest numbers of men who have sex with men (MSM) globally; however, geographic data on sexually transmitted infection (STI) prevalence and associations with sexual behavior are limited. Six-hundred and eight MSM in Chennai and Mumbai underwent screening for a behavioral trial and were assessed for bacterial STIs (syphilis, chlamydia, gonorrhea), HIV, and past-month self-reported condomless anal sex (CAS). Mumbai (37.8%) had a greater prevalence of any STI than Chennai (27.6%) (prevalence ratio [PR] = 1.37, 95% CI: 1.09, 1.73). This pattern also emerged for gonorrhea and chlamydia separately but not syphilis. Conversely, Mumbai MSM reported lower rates of CAS (mean = 2.2) compared to Chennai MSM (mean = 14.0) (mean difference = -11.8, 95% CI: -14.6, -9.1). The interaction of city by CAS on any STI prevalence (PR = 2.09, 95% CI: 1.45, 3.01, p < .0001) revealed that in Chennai, higher rates of CAS were not associated with STI prevalence, but in Mumbai they were (PR = 2.49, 95% CI: 1.65, 3.76, p < .0001). The higher prevalence of bacterial STIs but lower frequency of CAS in Mumbai (versus Chennai), along with the significant interaction of CAS with city on STI rates, suggests that there are either differences in disease burden or differences by city with respect to self-reported assessment of CAS. Regardless, the high prevalence rates of untreated STIs and condomless sex among MSM suggest the need for additional prevention intervention efforts for MSM in urban India.