Quality is a major current needs and requirements for any university system. The funding that universities receive a relevant influence on the scientific productivity of these. Thus the main objective of this study is to classify the Spanish regions in terms of scientific productivity and economic efficiency of their universities. It followed the same procedure used to prepare the 2009 ranking of research productivity in Spanish universities. The results show that there are differences in the classifications made on the basis of productivity and efficiency in the investigation. The more efficient Spanish regions in managing its resources to obtain research results are Catalonia, Asturias, Aragon, and Cantabria. From the results, each region can compare their situation with the rest and analyze strengths and weaknesses in research in terms of resources.