The Capes Thesis Prize indicates the quality and behavior of Graduate Programs, by selecting and awarding the best doctorate thesis in Brazil. This article presents an overview of the theses awarded between 2006 and 2009 and identifies highlights pertaining to institutions, area of knowledge and regions of Brazil. It was found that the academic community has yet to explore the Prize as a parameter for the recognition of research quality and should encourage the submission of greater number of theses. The Southeast has the greatest relative participation in the prize process and the best performance in relation to Honorable Mention, Prize and Grand Prize awards. By way of contrast, the North received no awards. A General Index of Institutional Classification was created and the most prominent institutions were: USP, Unicamp, UFMG, UFRJ, UFRGS and UNESP.