A γ-cyclodextrin (γ-CD) modified micellar electrokinetic capillary chromatographic (CD-MEKC) method has been developed to separate PAH metabolites. Baseline resolution of six acidic PAH metabolites was achieved within 14 min. The effects of several separation parameters were investigated in detail. These were the γ-CD concentration, sodium dodecyl sulfate (SDS) concentration, pH of the buffer, organic modifier, and urea concentration. The apparent capacity factors (k′app) increased linearly with SDS concentration which was consistent with theory. Possible mechanisms that account for the differences in the apparent distribution coefficients (Kapp) were proposed. The CD-MEKC method was compared with a capillary zone electrophoresis (CZE) method that we developed previously for the separation of the PAH metabolites.