Perchlorate (ClO4-) and other chlorine oxide anions were observed to complex weakly with hexamethonium (1,6-bis-(trimethylammonium)-hexane) in both aqueous and polar nonaqueous solvents. The resultant positively charged complexes were resolved by NACE using 2-propanol/acetone electrolytes prior to mass spectrometric detection using an Agilent(3D)CE system coupled to a Bruker Esquire 3000+ quadrupole IT mass detector. Using electrokinetic injection, the method detection limit for perchlorate in nonaqueous media was 10 mu g/L. The isotope patterns due to the presence of Cl-35 and Cl-37 in complex mass spectra allowed for unambiguous identification of perchlorate, chlorate (ClO3-), chlorite (ClO2-), and chloride (Cl-) in photoreaction samples.