The influence of para and meta substitution of benzylamine analogues on their interaction with bovine liver monoamine oxidase B has been investigated to provide insights into the nature of the substrate binding site. Binding data with para-substituted benzylamine analogues show the area of the binding site about the para position to be hydrophobic and exhibiting some steric constraints. Alkylation of the benzylamine nitrogen with methyl groups results in a dominance of steric constraints about the para-position as an influence on binding. meta-Substitution of the benzylamine ring results in a decreased binding affinity which exhibits a dependence on the van der Waals volume of the substituent indicating steric constraints also occur about this area of the bound substrate. The independence of the rate of enzyme reduction with the nature of the meta-substituent suggests these benzylamine analogues are bound in the substrate site in a manner which optimizes overlap of the pro-R benzyl C-H bond with the lone pair orbital on the nitrogen. In contrast, the observed rates of enzyme reduction by para-substituted benzylamine analogues exhibit a dominant steric dependence which suggests the mode of binding of this class of analogues does not provide this optimal overlap for efficient C-H bond cleavage. Support for this conclusion also comes from the observation that para-substituted N,N-dimethylbenzylamine analogues are competitive inhibitors and not substrates for monoamine oxidase B while the meta-substituted analogues are substrates, albeit poor ones. The demonstration of a tunneling contribution to the C-H bond cleavage step demonstrates the absence of any motion or changes in solvation coupled with that catalytic event and the close proximity of the enzyme group accepting the H to the pro-R position of the bound substrate. Little or no influence of meta or para benzylamine substituent on the rate of O2 reaction with the reduced flavin-protonated imine complex is observed which suggests alterations in the configuration of the bound substrate do not influence the reactivity of the reduced flavin.