The overall partition coefficients of the acid and amine components of amino acid derivatives, the substrates for proteinase-catalyzed synthesis of oligopeptide precursors, in an aqueous/organic biphasic system were studied both experimentally and theoretically. In a single-component system containing either an acid or amine component, the overall partition coefficient was well expressed by a model using the acid dissociation constant and partition coefficients for the non-ionized and ionized forms of the component. The overall partition coefficient in a binary-component system containing both acid and amine components was well simulated by the model when the formation of ion-pair complexes in the organic solvent phase was taken into consideration in addition to the partitioning of the non-ionized and ionized forms of the components. The formation of ion-pair complexes in the organic solvent phase was indicated by an analysis using Fourier transform infrared ray spectroscopy (FT-IR). In addition to the partition equilibrium, the aqueous-phase pH change after partitioning could be predicted by the model.