More and more attention is currently given to the sustainability of biofuels. Especially the greenhouse gas (GHG) reduction that is achieved with different biofuels is getting increased attention. GHG savings may vary significantly for different biofuels, and the EU and several Member States are looking for options to differentiate between biofuels according to their actual GHG savings. The European Fuel Oxygenates Association (EFOA) now wants to draw attention to an omission of current life cycle analyses (LCAs). LCA studies, even detailed well-to-wheel analyses, assume that ETBE and bio-ethanol replace MTBE and/or gasoline, and that the base gasoline is not changed. In reality, however, refiners will adjust their refinery operation when bio-ethanol or ETBE is added, because of the different characteristics of these products. EFOA has therefore asked CE Delft to conduct a study to investigate this issue. The study looks at two scenarios: substitution of MTBE and gasoline components a) by 5 vol% ethanol, or b) by an equivalent amount of ETBE. The GHG emissions of these scenarios were compared with each other, and with the emissions of the reference situation in which no ethanol is used. For the calculations a refinery model was set up, based on data and information from literature. The results indicate that the net effect of these refinery modifications on the GHG emissions is positive, i.e. GHG emissions reduce in both cases. The emission reduction is significant in the case of ETBE. This is mainly due to the high RON of ETBE, which allows for less severe process conditions in the refinery processes and hence lower energy consumption. This advantage for ETBE is to some extent undone by the higher GHG emissions related to production of ETBE and the production of extra isobutylene. We recommend to consider including this effect in the biofuel CO2 tools currently being developed, and to include an estimate of effects on refinery operations in future LCAs on ethanol and ETBE.