Public policies and services, such as education, health, welfare, infrastructure and sanitation, are increasingly developed and provided via different levels of government (national, regional and local), creating co-ordination and governance challenges. This report describes how Brazil’s 33 courts of accounts can use their oversight function – including audits – to help make such decentralised policies more effective and coherent. It presents the results of a 3-year project to improve how the courts can work together, using the area of education as a pilot for testing the use of indicators in the strategic selection of audits. The report offers a model for audit institutions to assess multi-level governance, and explores governance models for stronger collaboration among the courts of accounts in Brazil. These approaches may inspire and inform other supreme audit institutions with responsibilities for auditing decentralised policies and programmes involving central, regional and local governments.