Previous data show that the effects of clozapine on regional brain activity are different from those of other antipsychotic agents. It seemed of interest to study the brain activity patterns after treatment with clozapine, since this drug might correct basal deficits directly related to schizophrenia or instead induce changes that would in some way compensate distant abnormalities. In order to study the activity pattern resulting from clozapine treatment we have used FDG-PET and statistical parametric mapping (SPM) to explore the functional status of patients after chronic treatment with this drug, We compared their metabolic activity with normal controls and neuroleptic-naive (NN) patients, with the aim to identify if a reversion of pre-existing deficits or a induction of different changes was the result of clozapine administration. We compared metabolic patterns in 23 treatment-resistant (TR) patients after 6 months of treatment with clozapine, eighteen healthy subjects, and 17 NN schizophrenia patients. After treatment with clozapine, TR patients showed a clear hypofrontality and caudate hypometabolism in comparison with both the controls and NN patients, and also a lower thalamic activity than the healthy controls. In conclusion, our results support a preferential role for prefrontal regions and their subcortical connections in the mechanism of action of clozapine, resulting in a clearly hypofrontal state as compared to both controls and schizophrenia patients without previous treatment.