Introduction. Second-generation antipsychotics treatment is associated with weight gain and metabolic disturbances. Although much research has been done on the topic, the precise mechanisms underlying such side effects are still not well understood. Method. We followed over 16 weeks a group of 17 schizophrenia patients who were treated with olanzapine and monitored biometric, clinical, and metabolic data, including ghrelin and leptin levels. All patients had a structural cerebral magnetic resonance imaging examination during the first week of their followup and at the end of the study. Results. We found positive and negative significant correlations between grey matter volumes of several brain regions and variations of body weight as well as of ghrelin and leptin levels. The right frontal operculum, bilateral precuneus, and bilateral hippocampal regions were found to be significantly associated with those changes. Conclusion. Our results suggest associations between brain structure and metabolic variations in schizophrenia patients taking olanzapine.