Merging aqueous two-phase systems (ATPS) with high throughput screening techniques is a promising approach which will certainly lead to a more frequent use of ATPS both in industry and in research. Despite the diverse possible applications of polymer-polymer or polymer-salt based extraction systems for biotechnological downstream processes the use of these systems has so far been limited. This is mostly due to the poor predictability and the large number of parameters influencing the partitioning result. Especially the large number of possible parameter combinations makes robotic high throughput screening an interesting alternative to manual experiments. Methods using the robotic pipetting station Tecan Freedom Evo 200 for the development of ATPS processes are described in this paper. Characteristic values such as tie lines, binodal curve and volumetric measurement are essential for the characterization of this kind of systems and can successfully be determined by the robotic system. Most important, the measurement of protein concentrations, partition coefficients and yields could also be automated and parallelized offering the possibility to design ATPS processes while screening a broad range of parameters with a high sample throughput. (c) 2007 Elsevier Ltd. All rights reserved.