This study was intended to assess the existing Information System (IS) of Primary Health Care (PHC) programs, as an example of vertical health programs, in Sudan, specifically the Northern State. Particular attention was paid to the issue of fragmentation of the IS, and opportunities and challenges to integrating it.The study adopted case study design and data were collected through interviews, analysis of relevant documents, and observation of the settings. The results were analyzed using interpretive approach.The findings of the study revealed that PHC programs IS is ineffective at providing good quality information that is convincing for managers to use to support decision making. The main problems of the system included lack of good infrastructure, inadequate skilled personnel, parallel reporting and lack of coordination. Absence of supportive supervision and feedbacks to lower levels were also major problems contributing to IS dysfunction.Our study also showed that effort to integrate PHC programs IS might be challenged by absence of uniformity of data handling procedures, and lack of decentralized information management. Adding to the challenges is the difference in interests of the programs’ stakeholders as for integration of their IS. On the other hand, opportunities for integration of the programs’ HIS lie in the existence of Health Information Center (HIC) which receives collected health data from all parts of the state. Besides, most of the study participants were expressing optimism at outcomes of IS integration.Therefore, this study intended to inform efforts to integrate the existing PHC programs IS, of challenges and opportunities in the structural, socio-cultural and political contexts of the organization.