Within the scope of this thesis, the application of ionic liquids (IL) for the generation of aqueous two-phase systems (IL-based ATPS) and their use for the purification of catalytically active enzymes was evaluated. By studying the partitioning of different model proteins, a deeper understanding of the mechanisms influencing the partition process is provided. The IL AmmoengTM 110 in combination with an inorganic salt (K2HPO4/KH2PO4) can be used to establish an IL-based ATPS for the selective purification of two alcohol dehydrogenases. The presence of IL within the system was found to be advantageous due to its stability enhancing effect on both enzymes and its solubility enhancing effect on hydrophobic substrates. Thus, IL-based ATPS offer the opportunity to combine the purification process of active biocatalysts with the performance of enzyme-catalysed reactions.