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Background: Santos Metropolitan Region (SMR), State of Sao Paulo, historically is well known as being one of the areas with the largest number of AIDS cases in Brazil, especially among injection drug users (IDUs). The main objective of this study was to assess the effects of changes in drug-using patterns among IDUs on trends in HIV infection among IDUs in the 1990s., Methods: During 1991 through 1992 (wave 1; n = 214), 1994 through 1996 (wave 2; n = 135), and 1999 (wave 3; n = 108), we conducted three cross-sectional studies of IDUs. All participants were interviewed and tested for antibodies to HIV., Findings: The overall sample population was 69% male, and 87% of the sample population was under 40 years old. Eighty-four percent of the population had less than 9 years of education. HIV seroprevalence was 63% in wave 1, 65% in wave 2, and 42% in wave 3 ( p <.001). Smoking of crack cocaine increased from 11% in wave 1 to 60% in wave 2 and 67% in wave 3 ( p <.001). The prevalence of frequent injections (>5 per day) decreased from 42% in wave 1 to 30% in wave 2 and 15% in wave 3 ( p <.001)., Interpretation: HIV prevalence decreased as injection frequency decreased and crack cocaine use increased. In SMR, patterns of drug use have been affecting the HIV epidemic more than scant public health intervention.