Similarities and differences between mitochondrial monoamine oxidase (MAO) substrates and inhibitors (both A and B types) are considered, studying quantitatively two molecular properties: electron density and molecular electrostatic potential (MEP). The following molecules are considered: substrates: PHEA, BZA, tele‐N‐methyl‐histamine, phenylethanolamine, phenylpropylamine, tryptamine, dopamine, phenoxylethylamine, noradrenaline, serotonin, and p‐nitro‐phenylethanolamine; inhibitors: Deprenil, Clorgyline, and Lilly 51641 (only the moiety involved in the A–B differentiation is considered). The wave functions needed to calculate the analyzed properties are of ab initio quality, and have been calculated in analogous conformations, all near the energetic minima. Electron densities distributions are qualitatively compared by means of a correlation coefficient defined over the whole space. Otherwise, patterns of the possible zones of electrostatic interactions are described by means of the distances and angles between minima, in order to differentiate MAO‐A and MAO‐B substrates. The results reproduce efficiently the experimental classification and enable us to predict the type of enzymatic action of molecules not yet experimentally classified. Copyright © 1983 John Wiley & Sons, Inc.