We view innovation as a productive process, with outputs and inputs. We aim at compare the productivity of innovation across the twenty seven Member States of the European Union (EU-27), having a particular focus on Portugal. The data on inputs and outputs of innovation were collected from the Innovation Union Scoreboard 2010 report and covers the EU-27 Member States, from 2006 to 2010. The Total Factor Productivity index (TFP index) was used as the technique for data analysis. The choice of this technique was mainly determined by its flexibility and by data constraints. Two types of TFP indexes were computed: i) TFPt (time), which compares the productivity of innovation in each Member State with its productivity in a base year; ii) TFPs (space), which compares the productivity of innovation in each Member State with the productivity of the EU-27 average. Results show larger TFPs differences across Member States than TFPt differences. Concerning TFPt, there is a reduction of productivity of most of the Member States during the time length, which can be explained by the recent world financial crisis. This was the case of Portugal, where average TFPt in the time length is slightly below 1. The seven Member States that did not lose any productivity are mostly from Eastern Europe, Member Sates which have entered the European Union and accede to its structural funds more recently. Concerning TFPs, Portugal presents average TFPs well above 1. The Portuguese average TFPs value is close to the one of Germany and higher than the one of Sweden. The Innovation Union Scoreboard 2010 report classifies Portugal as Moderate innovator and Germany and Sweden as innovation leaders. We conclude that productivity of innovation in Portugal is similar to the one of Germany and higher than the one of Sweden. Differences between Portugal and those Member States, such as the ones reported in the Innovation Union Scoreboard 2010, can be explained by the fact of Portugal having fewer resources allocated to innovation and thus fewer outputs from innovation than Germany or Sweden have.