Since the eighties, case mix evaluation methods based on diagnosis-related groups (DRG) were gradually introduced in developed countries. These methods of assessing the costs of diseases to measure the productivity of the hospital have been introduced in management softwares that are not accessible to low-income countries. In this study, the authors applied these methods to an open source hospital management information system (HMIS) implemented in three university hospitals in Great Lakes Africa. A comparative study of the financial burden of five major diseases, monitored as part of a universal health coverage (UHC) analysis, was carried out. The level of coverage of patients in the hospitals was evaluated and the impact of UHC policies demonstrated. Although the financial protection of patients treated in the three hospitals had improved, HIV and tuberculosis treatments that ought to be free, remained a considerable financial burden for the patient.