Aqueous biphasic systems (ABSs) based on ionic liquids (ILs) have been considered as promising for the extraction, purification and separation of a wide range of substances, including biomolecules. Among the structurally modified ILs, amino acid ILs (AAILs) attract special attention. In this work we obtain systematic experimental data on the partitioning of L-tryptophan in the aqueous mixtures of 1-alkyl-3-methylimidazolium AAILs, [C _nmim]X, with different hydrocarbon chain length (n = 4, 8) and amino acid anions: X = [Leu] (L-Leucinate), [Val] (L-Valinate), [Lys] (L-Lysinate), and inorganic salt (K ₃PO ₄). Our results show that the partition coefficients are higher in the ABSs with AAILs than with halide ILs. AAIL with [C ₈mim] ⁺ cation demonstrate a noticeable specificity of lysinate anions. The obtained new data are discussed in terms of AAIL's structure. We conclude that hydrogen bonding is likely to play the major role in partitioning of the solute. Taking into account the low toxicity of AAILs, these ABSs have a high potential for the extraction of small biomolecules. Moreover, we found that in the studied ABSs based on chiral AAILs, partitioning of D-tryptophan is equal to that for L-tryptophan. ePC-SAFT is applied for the first time to model liquid-liquid equlibrium in ternary ABSs containing AAILs and partitioning of L-tryptophan. We obtain satisfactory results and conclude that ePC-SAFT is a promising tool for modeling ABSs that contain AAIL and inorganic salt.