Aqueous Two-Phase Systems (ATPS) is a primary recovery technique that has shown great potential for the efficient extraction and purification of high value biological compounds. The main advantages of this technique include scaling up feasibility, process integration capability and biocompatibility. In this review, the efficient use of ATPS for the extraction of proteins, genetic material, low molecular weight compounds, bioparticles, nanoparticles and cells is highlighted. The important role of ATPS in process integration, i.e., extractive conversion, extractive fermentation, cell disruption integrated with product recovery, and extractive purification, is discussed. A novel approach to protein molecular characterization combining ATPS and 2-dimension electrophoresis (2-DE) is introduced as a first step in the process development. Novel approaches for downstream processing using ATPS and dielectrophoresis are presented. Finally, trends concerning the application of ATPS strategies to address the future challenges of bioseparation are discussed.