Capillary electrochromatography (CEC) is an emerging technique that can be applied to the separation of neutral compound mixtures and provides a versatile alternative to micellar electrokinetic chromatography. In this paper, CEC is applied to the separation of polycyclic aromatic hydrocarbons (PAHs) and in vitro reaction products of PAH deoxynucleoside adducts. Some unique features related to CEC, such as convenience of stopping the flow, nanoliter flow rate, and low sample consumption, are discussed. On-column focusing in CEC can be conducted by introducing the analytes in a solution of lower solvent strength followed by elution with a stronger mobile phase, in a manner analogous to that used in normal HPLC (e.g., a 10-fold preconcentration factor can be readily achieved). Coupling of CEC to mass spectrometry for the detection of a relatively dilute DNA adduct mixture solution (10(-6) M) using the on-column focusing method is also presented.