Evidence implicating myelin related genes in the pathophysiology of schizophrenia is accumulating. Abnormalities of brain structure at the onset of psychosis may be related to variation in genes such as myelin associated glycoprotein (MAG). Subjects with first episode schizophrenia (n = 30) or schizoaffective disorder (n = 11), and healthy comparison subjects (n = 43) participated in an MRI scan. Two single nucleotide polymorphisms (rs720309, rs720308) in the MAG gene were genotyped. MAG genotype variation predicted cortical gray matter volume in first episode schizophrenia patients (p = 0.039), but not in controls (p = 0.827). Cortical gray matter, total gray matter, total white matter, and ventricular cerebrospinal fluid volumes did not differ between groups. Genetic variation in the MAG gene may predict cortical gray matter volume differences in patients in the first episode of schizophrenia or schizoaffective disorder.