The atypical antipsychotic clozapine has been reported to be metabolised mainly to its N-oxide and N-demethylated products. Brain, the target organ of clozapine, is known to contain numerous drug-metabolising enzymes which could alter the local concentrations of the drug. The metabolism of clozapine was, therefore, studied in rat brain preparations. Clozapine N-oxide was the major metabolic pathway in rat brain. We characterised the N-oxygenation of clozapine by rat brain preparations. The Km and Vmax values were found to be 319.6 microM and 28.1 pmol/min/mg protein, respectively. The formation of clozapine N-oxide was shown to be inhibited by thiourea (a flavin-containing monooxygenase inhibitor) but not by ketoconazole, quinidine or furafylline. This finding suggests prominent involvement of FMO in the N-oxygenation of clozapine in rat brain. This conclusion was further confirmed by the observation that the formation of clozapine N-oxide is sensitive to heat treatment of the brain preparation and can be partially protected from thermal degeneration by the presence of an NADPH generating system. It was further observed that the rate of clozapine N-oxygenation was much higher at pH 8.5 than at pH 7.4. Taken together, the data suggest that N-oxygenation is the major metabolic pathway catalysed by rat brain and this reaction is catalysed mainly by FMO. As significant interindividual differences have been observed in brain FMO activities, these differences may contribute to the interindividual differences in patient response to clozapine.