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Four <jats:italic>BDNF<\/jats:italic> polymorphisms were genotyped and analyzed versus 39 brain volume measures in 96 patients with schizophrenia or schizoaffective disorder and 104 healthy subjects. In all subjects, quantitative data on segmented gray, white, and cerebrospinal fluid (CSF) tissue class volumes of total brain and major cerebral lobes including ventricular CSF were obtained using magnetic resonance imaging (MRI). In a randomly selected subset of this population (n\u2009=\u2009101\u2013122), MR volumes from cerebellar tonsil, hemispheres, and vermis subregions, striatal structures, hippocampus, and corpus callosum were also measured. The <jats:italic>BDNF<\/jats:italic> 11757 G\/C polymorphism was highly significantly associated with frontal gray matter volume variation in patients alone and in patients and control subjects combined. In patients only, the 270 C\/T polymorphism was associated with total caudate volume. Significant associations were demonstrated between the <jats:italic>BDNF<\/jats:italic> 11757 G\/C and Val66Met polymorphisms and a global haplotype estimate of four <jats:italic>BDNF<\/jats:italic> polymorphisms and the posterior superior cerebellar vermis volume in the controls as well as in the combined group, but not in the patients. The 11757 G\/C polymorphism was associated with cerebellar hemisphere white and gray matter volumes in the combined group. The <jats:italic>BDNF<\/jats:italic> \u2212633 T\/A polymorphism was associated with gray matter of the putamen in the controls. Trends for associations between several polymorphisms\/haplotype estimates and MRI volumes were found. <jats:italic>BDNF<\/jats:italic> gene variation may influence brain morphology. 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