In this work, we investigate which countries have been more central during Phases I and II of the European Emission Trading Scheme (EU ETS) with respect to the different types of accounts operating in the system. We borrow a set of centrality measures from Network Theory's tools to describe how the structure of the system has evolved over time and to identify which countries have been in the core or in the periphery of the network. Performing partitions on the different types of accounts and transactions characterizing the EU ETS, we investigate whether intermediaries have affected the overall structure of the system. From the analysis of the European Union Transaction Log data over the period 2005–2012, we find that some national registries (France, Denmark, Germany, United Kingdom, The Netherlands) were much more central than others in the network. Empirical evidence, moreover, shows that some account holders strategically opened additional accounts in the more central registries, thus reinforcing their centrality in the network. Finally, it turns out that Person Holding Accounts (PHAs) have played a prominent role in the transaction of permits, heavily influencing the configuration of the system. This motivates further research on the impact of non-regulated entities in the EU ETS design.