The objective of the study was to adapt and apply an instrument to measure the organizational features of the primary care system in the municipality of Petrópolis. The study compared the performance of the new Family Health Program (Programa Saúde da Família or PSF) with traditional primary care facilities using data from facility surveys and key informant interviews. The main results include: (a) the methodology was capable of distinguishing between the two types of primary care services in the municipality; (b) the PSF clinics scored higher on most dimensions of primary care, although in some areas the traditional health units had equivalent scores; and (c) data obtained from interviewing key informants was generally compatible with that obtained by conducting facility surveys. The results suggests that in spite of making important advances in primary care, the municipality of Petrópolis continues to face several challenges including the need to improve access, enforce the gatekeeper role of primary care, and improve the coordination and community orientation of both types of primary care services. The methodology could be used to set objectives and monitor progress towards improving the organization and delivery of primary care in Petrópolis and elsewhere.