The measurement of protein binding of highly hydrophobic molecules is challenging due to poor solubility and strong adsorption, and further complicated by the competition of lipophilic partition in biological systems. Here, an attempt is presented to simultaneously simulate protein binding and lipophilic partition of hydrophobic molecules in a single system using CE. In this system, the incorporated biocompatible micelles also facilitate the protein binding study of hydrophobic molecules by enhancing their solubility (27 to 10(4) times) and eliminating the problematic adsorption. An equation is derived to describe the competition of protein binding and lipophilic partition and to estimate the protein binding constants in nonmicellar aqueous solution. Five polycyclic aromatic hydrocarbons (PAHs) and HSA were used as model hydrophobic compounds and protein, respectively. The study of the competition between lipophilic partition and protein binding reveals that the binding of the PAHs to HSA is governed by hydrophobic interactions and such binding (except naphthalene) can be eliminated by the lipophilic partition in the nonionic surfactant Tween-20. The developed method may be extended to evaluate the interactions of various macromolecules (receptors, enzymes, proteins, and DNA/RNA) and hydrophobic molecules.