This paper uses three different Malmquist Productivity Index (MPI) decompositions to measure Greek seaports’ productivity for the time period 2006-2010. In addition bootstrap techniques are applied in order for confidence intervals of the MPIs and their components to be constructed and therefore to verify if the indicated changes are significant in a statistical sense. Finally, a second stage nonparametric analysis has been applied identifying the effect of seaports’ size on their productivity levels.