A mathematical model based on the dissociation of charged compounds and the pH of each phase is developed to describe the partitioning of charged compounds in aqueous two-phase systems. Observed partition coefficients of several charged and uncharged compounds, including three pairs of oppositely charged analogs (tryptamine/indole 3-acetic acid, 5-methoxytryptamine/5-methoxyindole 3-acetic acid and 2-(p-tolyl) ethylamine/p-tolyl acetic acid), are compared in identical poly-ethylene glycol)/potassium phosphate aqueous two-phase systems over the pH range of 5.5 to 9.2. Among these pairs, the partition coefficients of the acids increased with increasing pH, from 8.4 to 33.3 for indole 3-acetic acid, from 11.4 to 53.9 for 5-methoxyindole 3-acetic acid, and from 4.2 to 17.7 for p-tolyl acetic acid. The amine partition coefficients also increased with increasing pH, from 4.0 to 7.8 for tryptamine, from 5.8 to 12.2 for 5-methoxytryptamine, and from 1.6 to 3.0 for 2-(p-tolyl) ethylamine, respectively. Consistent with the derived model, the greatest rate of increase in the partition coefficients of the acids occurs at low pH, while the greatest rate of increase in amine partition coefficients occurs at high pH. The ratio of partition coefficients for these pairs predicted by the model agrees with the observed partition ratio. The results indicate that charge, in addition to hydrophobic effects previously described, plays a major role in the partitioning of biological compounds.