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Higher education institutions in low- and middle-income countries are increasingly offering post-graduate degree programmes in health informatics. An analysis of accredited Master of Science in Health Informatics (MSc HI) programmes in the East African Community (EAC), a common higher education and labor zone, revealed wide variability in covered courses and competencies. In this paper, we describe the process undertaken to harmonize and establish common benchmarks for MSc HI for the EAC, in collaboration with the Inter-University Council for East Africa (IUCEA). After a multi-step process involving desk-reviews, benchmarking workshop with stakeholders, and quality assurance of benchmarks by IUCEA, the MSc HI benchmarks were finalized. These benchmarks outline the MSc HI degree programme goal, objectives, admission criteria, graduation requirements, and expected Learning Outcomes (ELOs). The ELOs are further translated into courses covering all identified skills and competencies. The benchmarks should facilitate mobility of students, faculty and labor, and improve program quality. [ABSTRACT FROM AUTHOR]