An electrophoretically mediated microanalysis (EMMA) approach, used to perform on-line chemistry between two small molecules, has been characterized and optimized. The plug-plug type EMMA method involved electrophoretic mixing and subsequent reaction of nanoliter plugs of kanamycin-containing samples and 1,2-phthalic dicarboxaldehyde and mercaptoacetic acid within the confines of the capillary column, which acts as a microreactor. Analyses were performed by pressure-injecting a plug of kanamycin sandwiched in two reagent plugs. A potential of 375 Vcm(-1) was then applied to electrophoretically mix the two reactants, and an incubation time of up to 5 min allowed the reaction to proceed prior to the application of a separation potential of 588 Vcm(-1). UV detection was at 335 nm. The background electrolyte was 30 mM sodium tetraborate at pH 10.0, containing 16% of methanol. The method was validated in terms of linearity, limits of quantitation and detection, and precision. The method allows determination of kanamycin in bulk samples as a fully automated procedure.