This paper introduces the Petri net for modelling and analysis of health systems where beyond the complexity of they activities, involves in its conception, implementation, operation and decision making several and differents professionals. The models are developed in PFS (Production Flow Schema) and MFC (Mark Flow Graph) that are interpretations of Peri nets aiming the explicit identification of resources and flow of itens (material and information). The services of the ambulatory of Clinic Hospital of University of São Paulo is considered in a case study to confirm the advantages of the proposal.