Given the importance of the control of sexually transmitted infections in the general population and specifically in the prison system, we rolled out this cross-sectional study in 2007. Standard questionnaires and blood samples were accessed among 680 prisoners. Protocol was approved by the Ethics Committee. Results: The prevalence: HIV, 1.8% (IC95% = 0.1–3.3); HBV, 21.0% (IC95% = 17.8–25.1); HBV, 5.3% (IC95% = 3.5–7.6) and syphilis 5.3% (IC95% = 3.5–7.6). Logistic regression identified association (p < 0.05): HIV: injectable drug use (OR = 15.4), over 30 years (OR = 13.3), cocaine use (OR = 5.4) and crack-cocaine use (OR = 5.2); HBV: injectable drug use (OR = 3.4), reference to previous sexually transmitted infection (OR = 2.3), over 30 years (OR = 1.9) and more than 5 years in prison (OR = 2.2); HCV: injectable drug use (OR = 9.65), marijuana use in prison (OR = 2.9) and more than 30 years (OR = 8.4) and for syphilis: homosexual relationship (OR = 7.8) and previous syphilis reported (OR = 7.7). These prevalences remain high when compared to the general population, however, HIV infection tended to decrease in prisoners while the other studied infections remained unchanged. Preventive actions to reduce sexual and parenteral risk have been advocated. However, measures capable of controlling these infections still have not made an impact.