In 2003, the process of public universities evaluation began.For this purpose, a set of performance indicators constructed by the Public University System (SUE by its acronym in Spanish) in alliance with the Ministry of National Education (MEN) was used.In an effort to know about the research efficiency level that public universities had in the period 2003-2012, an analysis of the results of these indicators was executed using Data Envelopment Analysis.In particular, the productoriented CCR model was applied.Although many universities have experienced a sustained development in some of the indicators analyzed and show high relative levels of efficiency, the results show that, as a whole, the Public University System has still much to improve regarding its scientific mission, especially, those aspects related to graduate programs and scientific journals.