CIDACS has received support from the Department of Science and Technology, Ministry of Health, Brazil; National Research Council (CNPq), Brazil and the Bill and Melinda Gates Foundation (CHAMADA MCTI/CNPq/MS/SCTIE/Decit/Fundação Bill e Melinda Gates N o 47/2014); Health Surveillance Secretariat, Ministry of Health, Brazil; Fundação de Apoio a Pesquisa do Estado da Bahia (FAPESB), Financiadora de Estudos e Projetos (FINEP), Secretaria de Ciência e Tecnologia do Estado da Bahia (SECTI) and Wellcome Trust.The Centre for Data and Knowledge Integration for Health (CIDACS) was created in 2016 in Salvador, Bahia-Brazil with the objective of integrating data and knowledge aiming to answer scientific questions related to the health of the Brazilian population. This article details our experiences in the establishment and operations of CIDACS, as well as efforts made to obtain high-quality linked data while adhering to security, ethical use and privacy issues. Every effort has been made to conduct operations while implementing appropriate structures, procedures, processes and controls over the original and integrated databases in order to provide adequate datasets to answer relevant research questions. Looking forward, CIDACS is expected to be an important resource for researchers and policymakers interested in enhancing the evidence base pertaining to different aspects of health, in particular when investigating, from a nation-wide perspective, the role of social determinants of health and the effects of social and environmental policies on different health outcomes.