Partition coefficients of amino acids, including glycine, alanine, 2-aminobutyric acid, valine, leucine, threonine, methinoine, tryptophan and tyrosine, in [C(n)mim]Br (n = 4, 6, 8) + K-2 HPO4 aqueous two-phase systems (ATPSs) have been determined, and the relative hydrophobicity of the equilibrium phases in the ionic liquids-based aqueous two-phase systems has been characterized by the Gibbs energies of transfer for methylene group from the bottom salt-rich phase to the top ionic liquid-rich phase. Based on these results, factors affecting the partitioning behavior of the amino acids have been investigated. It is shown that partition coefficients of the amino acids increase with the increase of hydrophobicity of the amino acids and the ionic liquids, solution pH value, tie-line length of the ATPSs and temperature of the systems. The possible driving forces and the thermodynamic parameters for the partitioning of amino acids in the ionic liquids-based ATPSs have also been discussed. (c) 2012 Elsevier B.V. All rights reserved.