The present investigation arises due to the limitation that exists in the determination and analysis of costs in health institutions which negatively affects the decision making on the best use of the available resources.As a solution to this problem, a methodology is proposed to calculate and analyze costs in the Pediatric Hospital of the city of Holguín, which serves as a tool for decision making. This result is based on the theoretical conceptions related to the costs in health institutions and the Methodological Guide for the Development of the Economic Evaluation in Health in Cuba, as well as the theoretical and empirical methods used in the research process. The methodology can be applied to pathology treatments and medical services with flexibility and adaptability to the context in which they are developed, which was evidenced in its application to the treatment of chronic otitis media and in the consensus of experts considered experts.