The strategic positioning of multipurpose public health organizations requires cost effectiveness and innovative dynamism. This study investigates the guiding principles of innovation in the Brazilian Leishmaniases Clinical Research and Surveillance Laboratory at the Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation. It examines three primary issues: cost reduction in healthcare procedures; cost effectiveness in resource distribution among healthcare, teaching, and research activities; and growth in relative technical efficiency within the organization. For the analysis of costs and expenses the Activity-Based Costing approach is adopted, whereas research distribution is analysed using the Spearman Test. Further, overall efficiency is studied through Data Envelopment Analysis. The main findings confirm that organizational innovation is driven by relative growth in technical efficiency. Such observed rationality in decision-making could be perceived as an alternative to the neoclassical hypothesis of short-run firm behavior. As such, the article empirically contributes to existing literature regarding guiding principle of innovation in health organizations.