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.