Objective To identify the main focus of research projects on malaria funded by Colciencias between 1995 and 2005. Methodology The Health Research Classification System (HRCS), developed by The UK Clinical Research Collaboration (UKCRC), was used for identifying the emphasis of research works on Malaria. Results During this period, research on malaria was mainly directed to etiology; the main cities benefited by the funding of research projects on malaria are institutions from Bogotá, Medellín and Cali. Conclusions These type of projects improve the strengthening of malaria research centers in areas such as molecular biology, production of vaccines, identification of resistance to antimalarial treatment, and climate change; some of the results obtained can affect policies and training of human resources on malaria.