Electrochemical oxidization mechanism of polyamides containing N-methylpyrrole and N-methylimidazole was investigated by electrospray ionization tandem mass spectrometry (ESI-MSn). The spectra of the oxidization products unambiguously revealed that one or two oxygen atoms are added to the polyamide after the bulk electrolysis. It was found that electrochemical oxidation preferably takes place on the imidazole ring of the polyamide with both imidazole and pyrrole to produce a carbonyl group on the rings. ESI tandem mass spectrometry has proven to be an excellent method for the structural identification of electrochemical oxidation products of DNA-recognizing polyamides.