Understanding the effects of health decentralization policies in Brazil requires different methodological approaches to capture the issue's complexity from distinct angles. Five case studies were thus performed to evaluate the degree of implementation of components related to decentralization of the health system management in selected municipalities (counties) in Bahia State, Brazil. A logical model was elaborated with definitions related to policy goals. A comparative study of the five municipalities, considered "exemplary cases", showed that decentralization alone does not explain the organizational changes in the municipal health systems. Local government characteristics such as the municipal master plan, governing capacity, and governance proved important for heath care changes. The main problems and insufficiencies were found in the system's management and quality of healthcare delivered to the population. The authors discuss their findings and identify critical areas for future interventions with special emphasis on the institutionalization of planning and evaluation and the development of inter-sector projects.