Two neutral cyclodextrins (CDs), hydroxypropyl-beta-CD (HP beta OD) and methyl-beta-CD (M beta CD), and two negatively charged forms, carboxymethyl-beta-CD (CM beta CD) and sulfobutylether-beta-CD (SB beta CD), were used to demonstrate the principle of separation of hydrophobic and non-charged polynuclear aromatic hydrocarbons (PAHs) by capillary electrophoresis (CE) based on differential partitioning of analytes between the CDs. The estimation of the partition coefficient (Ki) confirmed that the PAH components which partitioned most to the negative cyclodextrin (i.e. with the highest Ki) exhibited the longest migration time. The Ki values obtained for the CM beta CD-HP beta CD system are all below 1, indicating that the PAHs prefer to remain in the neutral HP beta CD. The Ki values for the SB beta CD-M beta CD buffer are all greater than 1, and cover a wider range, indicating preference of the PAHs for the anionic derivative. Methods were applied for separation of a PAH mixture containing various important PAHs on the US Environmental Protection Agency priority list. This novel procedure provided much better separation of PAH isomers, including benzo[a]pyrene and benzo[e]pyrene, than has been reported previously using CE. The system was applied to the sensitive determination of nanomolar levels of PAHs in contaminated soil.