Female sex workers (FSWs) have been documented to have high rates of sexually transmitted diseases and HIV in many parts of the world. However, little work has been done to characterize the prevalence of these infections along the U.S.-Mexican border, where sexual tourism and culturally sanctioned sex work among nationals is widespread. The objective of this study was to compare differences in background characteristics, HIV risk behaviors, drug use, and sexually transmitted infection/HIV prevalence between FSWs who participated in a behavioral risk intervention in two U.S.-Mexican border cities. Baseline data were collected from March 2004 through September 2005. Data from 295 FSWs were compared between Tijuana and Ciudad (Cd.) Juarez. Among 155 FSWs in Tijuana and 140 in Cd. Juarez, HIV seroprevalence was 4.8% and 4.9%, respectively. FSWs in Cd. Juarez were more likely to test positive for active syphilis (31.3%) compared with Tijuana (11.8%) but did not differ in terms of the prevalence of gonorrhea and chlamydia. FSWs in both sites reported high levels of unprotected sex and use of drugs; however, FSWs in Cd. Juarez were more likely than those in Tijuana to ever have injected drugs (75% vs. 25%, p <.001). Heroin and cocaine use and injection drug use were significantly more common in Cd. Juarez, whereas methamphetamine use was more common in Tijuana. Injection of vitamins was common in both cities. Logistic regression analyses suggested that being younger, working in Cd. Juarez, and using heroin or cocaine were independently associated with active syphilis infection. In Tijuana, methamphetamine use was strongly associated with active syphilis infection. These preliminary results suggest that risk profiles for HIV/sexually transmitted infection among FSWs in these two Mexico-U.S. border cities differ, suggesting a need to tailor interventions to the specific needs in each city.