Brazil has encouraged an ambitious set of policies towards the pharmaceutical industry, aiming to foster technological development while meeting health requirements. We characterise these efforts, labelled the ‘Complexo Industrial da Saúde’ (Health-Industry Complex, CIS), as an outcome of incremental policy change backed by the sustained efforts of public health professionals within the federal bureaucracy. As experts with a particular vision of the relationship between health, innovation and industry came to dominate key institutions, they increasingly shaped government responses to emerging challenges. Step by step, these professionals first made science and technology essential aspects of Brazil's health policy, and then merged the Ministry of Health's new focus on science, technology and health with industrial policy measures aimed at private firms. We contrast our depiction of these policy changes with a conventional view that relies on a partisan orientation of the executive.