The objective of this paper is to present the situational status of the National Health Research System of Peru (NHRS), the lessons learnt during the building process, the opportunities to improve it and the challenges. A description of the functions of the peruvian NHRS is done, in relation to governance, legal framework, research priorities, funding, creation and sustainability of resources and research production and utilization. It describes that in Peru we excert governance in research, we count with regulations, policy and research priorities, these last developed in the framework of a partipatory, inclusive process. The conclusion reached is that the challenges of the peruvian NHRS are to consolidate the governance and to develop the mechanisms to articulate the stakeholders involved in research, to improve the resources allocation for research and innovation, to ellaborate a plan for the development of human resources dedicated to research, to develop institutions and regional competences in order to perform research, and to link research in order to solve problems and make national research policies sustainable.