Monoamine oxidase (MAO) is an integral protein of the outer mitochondrial membrane, catalysing the reaction of oxidative deamination of monoamines in the central nervous system and peripheral tissues. The present paper reviews data on the structure of MAO, approaches and methods of computer modeling of active site structure, based on the analysis of MAO inhibition by selective inhibitors Flexible molecules, possessing many conformers are useless for computer modeling. Competitive fully reversible MAO inhibitors with rigid structure and limited number of conformers are preferential compounds for these studies.