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•There is an increasing urgency of decarbonising the EU transport sector.
•Biofuels are expected to play a significant role in the transition to a low-carbon economy.
•The EU has intensively promoted biofuels since 2000, reaching 5-6% of liquids consumption.
•Controversies have focused on indirect land use changes and competition with food production.
•In view of the scientific evidence, a new ILUC Directive was adopted in September 2015.