Long-term administration of antipsychotic drugs can induce differential expression of various proteins in brain cells, which may underscore the molecular mechanism of their clinical efficacy and/or side effects. We used two-dimensional gel electrophoresis in combination with mass spectrometry to screen differentially expressed proteins in the brain cells of rats under chronic clozapine treatment. We identified a protein, transthyretin, which was significantly up-regulated in the hippocampus of rats after four weeks' treatment of clozapine (20mg/kg) as compared with control animals. Western blot analysis further supported this finding. Besides, we also observed increased transcription of transthyretin mRNA in the cerebral cortex of rats under chronic treatment of clozapine (20mg/kg) or olanzapine (2mg/kg), but not haloperidol (1mg/kg), using real-time quantitative PCR. Transthyretin is a retinol carrier protein, our findings suggest that antipsychotic drugs treatment may affect the retinoid signaling cascade in the brain. Besides, transthyretin is also an indicator of nutritional status; increased transthyretin may be associated with the body weight gain of taking atypical antipsychotic drugs. This study also demonstrates that comparative proteome analysis is a feasible method to study the molecular mechanism of chronic antipsychotic drugs treatment.