Denmark introduced a restriction on trans-fats in food in 2003, but the Commission said the ruling would represent a trade barrier for suppliers from other member states.
It has given the Danish government an ultimatum to come up with a satisfactory public health argument for the ban or it will take the case to the Court of Justice.
Socialist and Green MEPs tried to get the case dropped on Thursday by proposing an amendment to a resolution on healthy living that is winding its way through Europe. They called for the Commission to drop its case - but failed to win enough support from fellow MEPs.
If the Commission succeeds, it could have far-reaching implications for national moves to encourage healthy eating across Europe. It might, for example, prevent any attempt by the UK government to enforce traffic-light signposting legally.
This week major supermarkets signed up to a BRC-led commitment to remove industrially added trans-fats from own-label products by the year end.