This study analyses the evolution of the technical efficiency of the public universities in Colombia. The paper uses the information provided by the System of management Indicators developed by the government, related to 32 public universities during the period 2003-2012. The factorial scores of factor analysis are used to estimate the efficiency, education and research indexes used in the study. To estimation the education and research technical efficiency, a panel data stochastic production frontier model is used, controlling for the capacity index. The model assumes time-varying technical inefficiency. Finally, quantile regression is used to classify universities on quartiles 25, 50 and 75, based on their high, medium or low efficiency level. The results indicate that both education and research indexes increase with financial resources, physical capacity and, especially, professorial capacity.