BackgroundPoor governance and accountability compromise young democracies’ efforts to provide public services critical for human development, including water, sanitation, health, and education. Evidence shows that accountability agencies like superior audit institutions can reduce corruption and waste in federal grant programs financing service infrastructure. However, little is know about their effect on compliance with grant reporting and resource allocation requirements, or about the causal mechanisms. This study protocol for an exploratory randomized controlled trial tests the hypothesis that federal and state audits increase compliance with a federal grant program to improve municipal service infrastructure serving marginalized households.Methods/DesignThe AUDIT study is a block randomized, controlled, three-arm parallel group exploratory trial. A convenience sample of 5 municipalities in each of 17 states in Mexico (n=85) were block randomized to be audited by federal auditors (n=17), by state auditors (n=17), and a control condition outside the annual program of audits (n=51) in a 1:1:3 ratio. Replicable and verifiable randomization was performed using publicly available lottery numbers. Audited municipalities were included in the national program of audits and received standard audits on their use of federal public service infrastructure grants. Municipalities receiving moderate levels of grant transfers were recruited, as these were outside the auditing sampling frame – and hence audit program – or had negligible probabilities of ever being audited. The primary outcome measures capture compliance with the grant program and markers for the causal mechanisms, including deterrence and information effects. Secondary outcome measure include differences in audit reports across federal and state auditors, and measures like career concerns, political promotions, and political clientelism capturing synergistic effects with municipal accountability systems. The survey firm and research assistants assessing outcomes were blind to treatment status.DiscussionThis study will improve our understanding of local accountability systems for public service delivery in the 17 states under study, and may have downstream policy implications. The study design also demonstrates the use of verifiable and replicable randomization, and of sequentially partitioned hypotheses to reduce the Type I error rate in multiple hypothesis tests.Trial registrationControlled-trials.com Identifier ISRCTN22381841: Date registered 02/11/2012Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2458-14-912) contains supplementary material, which is available to authorized users.