Evandro Chagas National Institute of Infectious Diseases (INI) has implemented Laboratories for Clinical Research Associated to Healthcare Assistance in Infectious Diseases, structures inspired on Innovative Organization of Mintzberg’s theory. In order to improve clinical research according to Integral Healthcare Model, INI’s Chagas Disease Clinical Research Laboratory has adopted this organizational innovation as an incentive mechanism based upon values of decentralization and entrepreneurial orientation. This case study uses, as methods to assess said innovation, surveying of micro costs, Activity Based Costing system, Spearman correlation test and DEA. Aggregates knowledge on the contribution of organizational values in multipurpose public health organizations and shows the effects of INI’s restructuring on development of research, diversification of healthcare and promotion of cost-effectiveness and overall efficiency.