Over the last years, aqueous two-phase systems (ATPS) regained an increasing interest due to their potential in the downstream processing of biomolecules. After many years with only a few articles published, a lot of effort and work has been put into studying these systems for the partitioning of a range of compounds including proteins, organic low-molecular weight molecules or metal ions. Although several research and review articles appeared, a background review on ATPS partitioning fundamentals is needed. In this article, partitioning theories and main effects of several important factors for partitioning, such as molecular weight of the polymer, effect of added salts, pH, electrical charges, and temperature on phase diagrams, tie-line lengths, interfacial tension and settling time of the two aqueous phases are extensively reviewed. The trend in ATPS research is given compiling the recent 2008–2013 research articles published in the field.