Ionic liquids (ILs) constitute a new generation of solvents entirely composed of ions. ILs are usually considered as green solvents due to their negligible vapor pressure and other properties, such as non-flammability and high thermostability. Biotechnological applications involving the use of ILs are currently emerging. Reports on enzymatic and whole-cell catalysis in the presence of ILs increased from the past decade. Nonetheless, IL decomposition at relatively low temperatures as well as IL toxicity towards microbial cells and superior organisms recently challenge the "green label" commonly attached to ILs. On the other hand, the possibility to fine-tune practically all the IL physicochemical properties by modifying its chemical structure makes IL truly designer solvents. Thus, IL tuning can be applied to overcome toxicity drawbacks and to broaden their application spectrum. This work reviews the use of ILs in biotechnological applications. Finally, critical niches for future research are identified and discussed. (C) 2010 Elsevier Ltd. All rights reserved.