The 5-hydroxytryptamine type-3 receptor antagonist tropisetron is in clinical use as an anti-emetic drug. This compound also exerts both potentiating and inhibitory effects on the glycine receptor chloride channel. The inhibitory effects occur at micromolar concentrations, whereas the potentiating effects are shown here to occur at femtomolar concentrations at the homomeric alpha1 receptor. Potentiation occurred only when tropisetron was applied in the presence of glycine. We also sought to identify molecular determinants of tropisetron inhibition at the alpha1 glycine receptor by serially mutating residues located in or near known ligand-binding sites. We discovered that conservative mutations to N102 ablated tropisetron inhibition without affecting the magnitude or sensitivity of tropisetron potentiation. Several lines of evidence, including a structure-activity analysis of tropisetron, atropine and SB203186, suggest that N102 may bind to the tropisetron tropane nitrogen via H-bonding. Mutation of the N125 residue in the beta subunit, which corresponds to N102 in the alpha1 subunit, had little effect on tropisetron inhibitory potency. These results show that N102 is required for tropisetron inhibition but not potentiation and that inhibitory tropisetron binds in different orientations at different subunit interfaces. To our knowledge, tropisetron is the most exquisitely sensitive modulator yet identified for a cys-loop receptor.