Sugar-based compounds are widely used in pharmaceuticals, cosmetics, detergents and food. They are mainly produced by chemical methods, but the use of enzymes as ‘a greener alternative’ to organic synthesis has been investigated for more than 20 years. Due to the low polar substrate solubility in organic solvents compatible with enzymes, research has focused on the application of substitutes for biocatalysis, especially ionic liquids (ILs). After introducing the main properties of ILs and especially their ability to solubilize sugars, this review focuses on one of their applications, the biocatalytic synthesis of carbohydrate derivatives. In this context, they can be used in pure IL systems, in IL/IL systems or in IL/organic solvent systems. Finally, this review provides an update on the environmental fate of ILs. Their exploitation in ‘green’ processes is still limited due to their low degradability but research is currently under way to design new more ‘eco-friendly’ ILs. Copyright © 2012 Society of Chemical Industry