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The scope of this paper is to contribute to the understanding processes, context and challenges of medical audit and its integration with cost management, quality and risk in the health sector. For this purpose a case study in the medical audit department of a medical professional cooperative, located in northeastern Brazil was conducted. This choice was strengthened by the interest in examining the issues of integration in an institution whose main goals are to preserve the professional enrichment and provide quality in health care. The interpretation of the results indicated that the main focus of attention is given to the accounts audit whilst minimum priority is giving to analytical auditing. The audit sector is not perceived by the members as an ally and there are no programs focused on the involvement of cooperative members with this area. The over- estimation of the auditor's experience may be inhibiting the investment in professionalization and in management models and more sophisticated auditing tools. Evidence-based medicine is used in a very restricted way. No effective audit integration with the information systems, the strategy of the organization, quality programs, cost management and use of evidence-based medicine was observed. [ABSTRACT FROM AUTHOR]