The number of papers dealing with the structure-based drug design is continuously growing, which demonstrates the importance of such tools in medicinal chemistry. In the current paper, the published literature concerning the use of the ligand-protein docking methodologies in the study of the monoamine oxidase (MAO) enzymes was reviewed. Ten years of studies aimed at developing new compounds active as MAO inhibitors (MAOIs) were covered. The literature regarding thiazole, caffeine, pyrazole, chromone, indeno-pyridazin, β-carboline, indole, coumarin, anilide and amphetamine derivatives, was discussed in some detail. It is apparent that, through this computational approach, more selective and potent molecules can be proposed as inhibitors by applying precise modifications on the basic scaffold.