The social determinants of the health-disease process and the challenge of comprehensive care have led the World Health Organization to propose Complementary and Alternative Medicines to be included in health policies. In Brazil in 2006 the National Policy on Integrative and Complementary Practices (PNPIC) was published. It is a tool for the institutionalization of homeopathy in the Unified Health System (SUS). This paper analyzes the knowledge of health managers of municipalities of São Paulo on PNPIC, and its influence on homeopathic care. In 2008, the municipalities that performed homeopathic consultations from 2000 to 2007 were identified in DATASUS, managers were interviewed and the results were analyzed quantitatively and qualitatively: of the 645 municipalities, 47 had offered homeopathy and 42 of them were interviewed. Of these, 26% knew about PNPIC, 31% knew little, 41% were unaware of it. It should be stressed that those aware of it stated that they use PNPIC to: instruct the local government about homeopathy; the construction of specific legislation and the increase in homeopathic services. The conclusion is that PNPIC is unknown by health managers and those that know it use it to make known the homeopathic medical rationale and justify its application in the SUS.