5,6-Dihydroxyindole (5,6-DHI) and a series of 4- and/or 7-methylated analogues of 5,6-DHI have been synthesized and evaluated for their ability to inactivate purified rat liver catechol O-methyltransferase (COMT). The inactivation of COMT by these agents could be prevented by excluding oxygen from the incubation of mixtures, indicating the necessity for their oxidation to the corresponding aminochromes. Substrate protection studies and kinetic studies suggested that the loss of enzyme activity resulted from the modification of a crucial amino acid residue at the active site of COMT through reaction with the quinoid oxidation products. The COMT inhibitory activity of the 4- and/or 7-methylated analogues of 5,6-DHI argue against a mechanism involving a 1,4 Michael addition reaction at positions 4 or 7 on the aminochrome. Considering the number of potential electrophilic centers on the basic aminochrome structure, the site of the reaction might change depending on the aromatic substitution pattern. The preferred pathway of reaction may be determined in part by the juxtaposition of the protein nucleophile to the possible sites of attack on the electrophilic ligand but also in part on the reactivity of the electrophilic site which might change with substitution on the aromatic ring.