The healthcare milieu of most developing countries is often characterized by multiplicity of health programs supported by myriad of donors geared towards reversing disease trends in these countries. However, donor policies tend to support implementation of vertical programs which maintain their own management structures and information systems. The emerging picture overtime is proliferation of multiple and uncoordinated health information systems (HIS), that are often in conflict with the primary health care goals of integrated district based health information systems. As a step towards HIS strengthening, most countries are pursuing an integration strategy of the vertical HIS. Nevertheless, the challenges presented by the vertical reporting HIS reinforced by funds from the donors renders the integration initiatives ineffective, some ending up as total failure or as mere pilot projects. The failure of the systems after implementation transcends technical fixes. This paper drew on an empirical case to analyze the challenges associated with the effort to integrate the HIS in a context characterized by multiple vertical health programs. The study revealed the tensions that exists between the ministry of health which strived to standardize and integrate the HIS and the vertical programs which pushed the agenda to maintain their systems alongside the national HIS. However, as implied from the study, attaining integration entails the ability to strike a balance between the two forces, which can be achieved by strengthening communication and collaboration linkages between the stakeholders.