Mildmay Uganda (MUg), an HIV treatment centre near Kampala, the capital of Uganda, has entered into a memorandum of understanding to collaborate with Canadian researchers at the University of Ottawa to develop their research programme and develop an observational cohort database (the MUg observational cohort). The primary objectives of the MUg observational cohort are to monitor clinical care and outcomes of HIV among patients on treatment and to bring awareness to trends that are functional and dysfunctional in HIV care in Uganda. The MUg observational cohort comprises 8835 individuals who initiated combination antiretroviral therapy at MUg between January 2004 and October 2011. There are considerably more women (63.2%) than men in the cohort, and age spans from newborn to 92 years old. The low median age of 31 years (interquartile range: 18-38 years) can be explained by the 24.9% of the cohort aged <18 years. The median baseline CD4 cell count among the entire cohort is 172 cells/mm(3) (interquartile range: 73-249 cells/mm(3)). Data are routinely completed at treatment initiation, and follow-up data are collected routinely through physician visits and laboratory results. Data comprise demographic, behavioural and clinical variables. Collaborations and enquiries relating to the MUg observational cohort are encouraged, and can be addressed to Dr Edward Mills at edward.mills@uottowa.ca.