A quantitative data set produced as part of the PrEPVacc Registration Cohort, a study to prepare a population of HIV negative individuals at risk of acquiring HIV for possible participation in the PrEPVacc HIV vaccine efficacy trial. Data was collected between July 2018 and December 2022 from a registration cohort located in Masaka, Uganda. Variables cover HIV incidence, and associated demographic and behavioural factors. Study data was collected by trained designated staff and entered directly onto the appropriate Case Report Forms(CRFs) or in source documents. A study database was set up in OpenClinica, a web-based data management system, and hosted at the MRC/UVRI clinical research centre. At the site, data was double-entered by two separate Data Entry Personnel. Data was entered as soon as possible (e.g. within one week) after a visit and routine data cleaning queries were raised and resolved. All data analysis was conducted in STATA V.18.