The paper addresses issues of the health sector rehabilitation in post-conflict situation, and in particular the role of Northern Non-Governmental Organisations (NNGOs) in this process. While armed conflicts are regarded as public health issues for their negative implications on health and health systems, post-conflict situation is considered, despite its complexity, as having both risks and opportunities for making the health system more equitable and sustainable. In this respect, NNGOs are believed to be able to play an efficient and effective role in rehabilitating the health system. The paper asserts that the assumed good qualities of the whole NNGOs sector in this specific context is not based on evidence and that a critical analysis is needed. Problems affecting NNGOs interventions are then highlighted. These include their political neutrality, technical accountability to policy, planning and quality development. These problems may have their roots at conceptual, operational and political levels. To avoid generalisations and unproved assumptions, research is therefore needed to distinguish NNGOs' characteristics, roles and motivations and to assess the extent to which NNGOs' interventions are effective in rehabilitating the health system in post-conflict settings as well as in strengthening local institutions.