This thesis, examines three research questions concerning the coherence between the European Union (EU) rules about State aid for environmental protection and the “polluter-pays-principle” (PPP) in the context of the free allocation practice in the European Union Emissions Trading System (EU ETS).  The aim of the first research question is to study whether the free allocation of emission rights within the EU ETS is compatible with the EU State aid rules. The conclusion to this research question is that the free allocation practice does fulfil the criteria to constitute State aid but that the Commission has permitted derogations against this prohibition, provided certain conditions such as necessity and proportionality are fulfilled.   The second research question is whether the free allocation method is compatible with the PPP. The PPP can be divided into an economic dimension and a legal dimension and it is concluded that the free allocation practice is contrary to at least the legal dimension of the PPP. According to the OECD, exceptions from the principle can be made but the EU has not established conditions for when such derogations from the PPP can be made.   The third research question concerns the compatibility between the EU State aid rules and the PPP. Generally there is no disharmony between the State aid rules and the PPP, since the PPP should not be seen as a mere prohibition against aid to polluters, but can also be considered a complement to State aid rules. However in the specific case of the free allocation rules in the EU ETS, State aid measures contrary to the PPP are carried out. Since the EU has not established conditions for whether derogations from the PPP can be made, it is concluded that the free allocation practice within the EU ETS does expose a disharmony between the PPP and the State aid rules. It is suggested that the EU clarifies the conditions for permitting derogations from the PPP, in preparation for the fourth phase of the EU ETS.