Significant differences in HIV-related risk behaviors have been found between Puerto Rican drug users in New York City (NY) and Puerto Rico (PR). An examination of HIV incidence rates and characteristics of seroconverters in each location was undertaken. Baseline and follow-up interviewing and HIV testing were conducted in 1998 to 2002 with seronegative Puerto Rican injection drug users (IDUs) and crack smokers from East Harlem, NY (n = 455) and Bayamón, PR (n = 268). There were a total of 32 seroconverters, 9 in NY and 23 in PR, for seroconversion rates of 0.88/100 person-years at risk (pyr; 95% CI, 0.31-1.45) in NY and 3.37/100 pyr (95% CI, 2.02-4.72) in PR (P < 0.001). In PR, variables significantly related to seroconversion were younger age and using shooting galleries. Being in methadone treatment was protective against seroconversion. In NY, crack use was significantly related to seroconversion. The higher seroconversion rate found in PR indicates a need to enhance HIV prevention efforts, including increasing methadone treatment and access to sterile syringes. The need to address sexual risk behaviors in both locations was also indicated. Resources focusing on reducing HIV transmission in the Caribbean should include efforts to target the drug use-HIV epidemic in PR.