Background: Iquitos Peru, a densely populated port city housing both a large military base and a booming tourist industry, provides a thriving market for commercial sex and, consequently, sexually transmitted disease (STD). The purpose of this study was to characterize the prevalence of gonococcal and chlamydial infections among commercial sex workers (CSWs) and to correlate those findings with social/behavioral characteristics. Methods: One hundred CSWs, recruited through street and brothel outreach, were administered questionnaires. Urine specimens were collected for gonorrhea and chlamydia testing using ligase chain reaction assays. Results: Twenty-eight percent of CSWs were positive for chlamydia (22%) or gonorrhea (14%). Registered CSWs were more likely to have worked more than 5 years (p = 0.03), report 10 or more partners (p = 0.002), and work in brothels (p < 0.001). Significant associations were also noted between infection status and age, with adolescents at increased risk (odds ratio [OR] = 4.13, p = 0.001), and duration of employment, with those employed less than 5 years at increased risk (OR = 3.72, p = 0.04). The latter association, however, was because of age. Also, most CSWs believed themselves to be at no/small risk or didn't know their risk of future gonococcal infection (30%/12% and 25%, respectively) and AIDS (25%/8% and 35%, respectively), with 11% perceiving AIDS as more of a threat. Conclusions: High infection rates, lack of knowledge regarding STD/HIV risk assessment, and other high-risk behavior prevalent among this population stress the need for STD intervention. The study further suggests that educational/risk assessment programs and risk reduction interventions could be successful.