Abstract Sodium dodecyl sulfate (SDS) is the most widely used surfactant in micellar electrokinetic capillary chromatography (MECC). The separation of highly hydrophobic compounds by MECC can be difficult because they will completely associate with the micelles and will elute at the end of the elution window. The addition of organic solvents to the running buffer may enhance the separation, but they can also inhibit micelle formation. An alternative is the use of different surfactant systems such as bile salts and ionic polymers. In this work, four different surfactants (SDS, sodium cholate, sodium deoxycholate and Elvacite 2669) have been studied by using two organophosphorus pesticides (chlorpyriphos-methyl and -ethyl) as model compounds.