The introduction of a methylene bridge between the phenyl and tetrahydropyridyl moieties of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) results in increased selectivity for monoamine oxidase B (MAO B) over monoamine oxidase A (MAO A). However, lengthening of this bridge results in a total loss of selectivity. In the present study, a number of isomeric 4-naphthyl-, 4-(naphthylalkyl)-, 4-thienyl-, and 4-(thienylalkyl)tetrahydropyridines, conformationally restrained and flexible analogs of MPTP, were synthesized and evaluated as potential selective substrates of MAO A and B. In terms of the parameter (turnover number)/Km, the bulky naphthyl analogs were invariably better substrates of MAO A than kynuramine, the reference substrate for this enzyme. In addition, all naphthyl analogs, regardless of conformational mobility, were more effective substrates of MAO A than MAO B. Similarly, all thienyl analogs were found to be more effective substrates of MAO B. In contrast to the naphthalenes, the conformationally restrained thiophenes 9a and 10a were found to be poor substrates of MAO B, relative to benzylamine, the reference substrate. These results suggest that the selectivity of these compounds for either MAO A or B is determined by the complex interplay of molecular size and flexibility. In this interplay, either one of these two factors may predominate.