There is inadequate information on the burden of HIV infection, and on the prevalence of the risk factors for HIV transmission among University students in Uganda. Routine sources of data such as HIV surveillance and national population-based AIDS Indicator surveys do not provide information on institutional populations such as University students. Moreover, these sub-populations require interventions to address the risk factors that expose them to HIV infection in their unique settings. In order to address this, the IUCEA conducted a baseline survey on HIV/AIDS in institutions of higher learning in Uganda. Similar studies were conducted in Kenya and Tanzania. The overall objective of the survey was to determine the prevalence of HIV and related risk factors among University students in Uganda. The survey provides information that will guide universities and their partners in mainstreaming HIV/AIDS prevention and control.