This paper presents the results of an efficiency study of Colombian public universities in 2012, conducted using the methodology of Data Envelopment Analysis (DEA) and the models CCR, BCC and SBM under output orientation. The main objective is to determine technical, pure technical, scale and mix efficiencies using data acquired from the Ministry of National Education. An analysis of the results shows the extent to which outputs of inefficient Higher Education Institutions (HEIs) could be improved and the possible cause of this inefficiency. The universities were also ranked using a Pareto efficient cross-efficiency model and a study was made of changes to overall productivity between 2011 and 2012. The results showed Tolima, Caldas and UNAD to be the best-performing universities, with Universidad del Pacífico as the worst performer. Malmquist index was applied to analyze the change in productivity from 2011 to 2012. The Universidad de La Guajira showed great improvement in technical efficiency between 2011 and 2012.