BACKGROUND: Incarcerated people carry a high burden of infection, including blood-borne diseases (BBDs). It is also known that one million people contract a sexually transmitted infection (STI) every day worldwide, which represents a global public health challenge. However, data regarding the prevalence of STIs and the risk factors among incarcerated populations are lacking. The objective of this study was to determine the prevalence and associated factors of BBDs and STIs among detainees in the largest pre-trial prison in Switzerland. METHODS: In a cross-sectional study conducted at the Champ-Dollon pre-trial prison, 273 male detainees answered a standardized questionnaire and were screened for syphilis, herpes simplex virus 2 (HSV-2), HIV, and hepatitis C (HCV). Prevalence rates and associations of BBDs and STIs with risk factors were computed. RESULTS: Most participants (90.9%) were migrants from outside Western Europe, and 5.9% were injecting drug users. HCV was diagnosed among 6.2% of participants (antibody prevalence). The prevalence of HCV was higher among injecting drug users (81.2%) than non-injectors (1.6%). The prevalence of HIV, syphilis, and HSV-2 was 0.4%, 1.1%, and 22.4%, respectively. HCV was associated with a history of injecting drug use and HSV-2 with a lower education level and being older than 26 years. CONCLUSIONS: This study showed the infection prevalence of 2-9 times higher among detainees than in the Swiss community. It also illustrated that these infections are associated with sociodemographic and risk factors. Therefore, the prison environment offers an opportunity to strengthen infectious disease control programs targeting specific subgroups of at-risk people. Such programs would benefit both the prison population and broader society.