Health information systems (HISs) serve as an indispensable foundation for developing health policy and strategies and improving delivery of routine health services in an evidence-based manner. In developing countries, HISs are not adequately functioning in spite of their important role such as monitoring tools for the progress of the Millennium Development Goals. This paper attempts to classify the HISs into four types according to their data sources. Information requirement by the diseases-specific funds (e.g. Global Fund to Fight AIDS, Tuberculosis and Malaria) and projects implemented by development agencies increase the workloads of health professionals at facility level and subsequently compromise data quality. For the data quality assurance and comparability of data across countries overtime of major health indicators, standardization of HISs are the urgent task.