This paper examines the productivity of Spanish public universities from 2002 to 2004. The used of the Malmquist Productivity Index illustrates the contribution of efficiency and technological changes to productivity change over the period. Separate analyses of teaching model, research model and knowledge transfer-model productivity are made. Moreover, some analysis about teaching quality, research quality and knowledge transfer quality are made to show how Spanish Higher Education System is developing their missions. Results suggest that on average the annual productivity growth was largely attributed to technological progress rather than efficiency improvements. Most of the productivity gain is attributed to improvements in research and knowledge transfer productivity rather than teaching