Ionic liquid-based aqueous two-phase systems (IL-ATPSs) are great candidates for the replacement of volatile organic solvents in liquid-liquid extractions. Besides, microfluidic separation techniques are a promising alternative to conventional systems since they provide continuous operation, better performance and easier capacity increase by a numbering-up approach. Herein, the advantages of IL-ATPSs and microfluidic continuous separation were combined within a microfluidic device with parallel flow allowing for the separation of the two phases at the exit of the microchannel. An aqueous solution of [C(4)mim] [BF4] and D-fructose was used as an IL-ATPS and compared with a conventional ATPS consisted of polyethylene glycol/salt solution. Based on the evaluated partitioning coefficient of a model substance, namely bovine serum albumin, the ionic liquid concentration and pH value of the IL-ATPS have been selected for the use within a pressure-driven microchannel system with y-shaped inlet and outlet. Furthermore, a three-dimensional model considering convection in the flow direction and diffusion in all spatial directions at steady-state conditions was developed, validated by experimental results and used to assess the feasibility of micro-scale parallel flow extraction in a wide range of flow rates. The chosen IL-ATPS was shown to be much more efficient media for continuous microfluidic extraction as compared to conventional ATPS, primarily due to much lower dynamic viscosity of IL-rich phase related to PEG-rich phase. (C) 2012 Elsevier B.V. All rights reserved.