I(2) site-selective compounds are known to interact with and inhibit monoamine oxidase (MAO), but it remains unclear as to whether this interaction occurs through an allosteric or competitive interaction. This study used the new selective, irreversible I(2) ligand BU99006, to clarify the relationship between MAO and the I(2) binding sites (I(2)-BS). Results demonstrate that irreversible binding of BU99006 to rat brain membranes does not inhibit the enzyme or interfere with its interaction with other imidazoline enzyme inhibitors. This finding suggests that the I(2) sites that react with BU99006 are not those implicated in MAO inhibition and points to the existence of at least two distinct I(2) binding proteins.