The Africa Medical and Behavioral Sciences Organization (AMBSO) Population Health Surveillance (APHS) is an open, longitudinal, population-based cohort including persons aged 13 years and above in diverse settings of rural, semi-urban and urban communities in Hoima and Wakiso districts in the Western and Central regions of Uganda. APHS is the first health and demographic surveillance system (HDSS) in Uganda that includes an urban cohort. Data are collected through face-to-face questionnaires covering a broad range of health-related issues including communicable and non-communicable diseases, risk factors and health determinants. Physical measurements and biological samples, e.g. for HIV status, are also collected. A baseline census was conducted in 2018/19 including 20 210 individuals. Of all 10 929 individuals eligible for the baseline survey, 4606 participated (42.1% participation rate). Follow-up rounds are conducted annually with possible mid-round phone surveys, such as one performed during the COVID-19 pandemic. APHS focuses on under-researched and emerging public health issues in Uganda, including mental health, substance use, gender-based violence (GBV), violence against children, food insecurity, health behaviours, disability and emerging diseases. Data collection from census activities and surveys target community types which exhibit considerable variation in risk behaviours and health conditions. AMBSO complements this research with qualitative work aiming to keep the APHS dynamic and responsive to changing needs.