As part of our efforts to characterize more fully the structural features of the monoamine oxidase (MAO) A and B active sites, we have examined the substrate and inhibitor properties of several 1-methyl- and 1-cyclopropyl-4-aryl-1,2,3,6-tetrahydropyridine derivatives with the human placental A and beef liver B forms of the enzyme. We find that the 4-(2-phenylphenyl) analog 23 exhibits a high activity and selectivity for MAO-A while the 4-(3-phenylphenyl) analog 22 shows activity only with MAO-B. Selectivities similar to those of the N-methyl series are observed with a series of N-cyclopropyl mechanism based inactivators. These results support a topological analysis which attempts to identify steric factors related to the reported substrate and inhibitor selectivities of these two flavoproteins and provide a better definition of the size of the active sites of the two enzymes.