A goal of pharmacogenetics is to clarify associations between allelic variation and risk factors in psychiatric illness. We report changes in regional brain metabolism based on dopamine alleles. Treatment-resistant schizophrenic subjects were positron emission tomography scanned with 18F-fluorodeoxyglucose after 5 weeks each of placebo and clozapine treatment. Significant regional brain metabolic effects were found for the D1 receptor genotypes (Po0.05), adjusted for multiple comparisons. Metabolic decreases for the 2,2 genotype but not the 1,2 genotype were observed in all major sectors of the brain, with the exception of the ventral parts of the caudate and putamen. Frontal, temporal, parietal, and occipital neocortices showed decreased metabolism as did the cingulate juxta-allocortex and the parahippocampal allocortex. Decreases were also observed in the thalamus, amygdala, and cerebellum bilaterally. No significant metabolic differences by genotype were observed for D3, 5HT 2A , and 5HT 2C polymorphisms. In terms of clinical response, the DRD1 2,2 genotype significantly improved with clozapine treatment, demonstrating a 30% decrease in the Brief Psychiatric Rating Scale positive symptoms in contrast to a 7% worsening for the 1,2 genotype (Po0.05). In this preliminary study, brain metabolic and clinical response to clozapine are related to the D1 receptor genotype. Molecular Psychiatry (2003) an association between parietal lobe, but not other major brain regions, volumes, and brain-derived neurotrophic factor (BDNF) alleles. 6 Laruelle et al 7 failed to find an association between D2 receptor binding and alleles at the TaqI-A RFLP site in the D2 receptor gene using single-photon emission computed tomography (SPECT) imaging. Despite their small sample sizes, these preliminary studies provide intriguing data regarding the ability of brain imaging to serve as an intermediate phenotype in pharmacogenetic studies. These studies, however, did not examine the relationship between allelic variation, clinical response to pharmacological treatment, and the intermediate phenotypes as revealed by brain imaging. The relationship between dopamine and serotonin receptor genotypes, regional brain metabolism, and clinical response to clozapine treatment was the focus of this study.We report the changes in brain metabolism based on dopamine and serotonin alleles following treatment with clozapine. Positron emission tomography scanning using 18 F-fluorodeoxyglucose (FDG PET) has the ability to measure regional brain metabolic response while the subject is performing an activation task. PET has the ability to resolve individual gyri and distinguish subcortical regions from each other. PET can measure brain work because of the close coupling between glucose utilization and neuronal activity. 8,9 During the FDG uptake, the subject performed an attentional task, the degraded continuous performance task (CPT), activating brain systems related to essential elements of the illness. In this task, subjects view a series of blurred num...