Background: Prescriptions for antipsychotic medications continue to increase, across many brain disorders, including off-label use in children, and the elderly. Recent animal data and uncontrolled human data suggest that antipsychotics may have deleterious effects on brain structure. The present study is the first to assess the effects of antipsychotics on brain structure in humans using a double-blind randomized placebo-controlled design. Methods: Participants were recruited from the multi-centre STudy Of the Pharmacotherapy of Psychotic Depression II (STOP-PD II, clinicaltrials.gov registration number NCT01427608). All participants had major depressive disorder with psychotic features ('psychotic depression') and were prescribed olanzapine and sertraline for a period of 12-20 weeks, which included 8 weeks of remission of psychosis and remission/near remission of depression. Participants were then were randomized to continue on this regimen or to be switched to placebo and sertraline for a subsequent 36-week period. Those who consented to the imaging study completed an MRI scan at the time of randomization and a second MRI scan at the end of the 36-week period, or sooner if the participant experienced a relapse. 88 participants completed a baseline scan; 75 completed a follow-up scan of which 72 were useable. Using mixed model regression, we assessed changes in gray matter morphology, and changes in white matter using diffusion-weighted MRI. We also explored the effects of illness relapse on the same measures. Findings: There was a significant treatment group by time interaction in cortical thickness, but not surface area, and thalamic, but not striatal or hippocampal volume. A similar interaction was found in mean diffusivity of white matter, but not fractional anisotropy. When the analysis was restricted to those who sustained remission only (controlling for effects of active illness and time), exposure to olanzapine compared to placebo was associated with significant decreases in cortical thickness and cortical surface area, but not subcortical volumes, no change in fractional anisotropy, but significant increase in mean diffusivity of white matter. Post-hoc analyses showed that those who relapsed on placebo experienced decreases in cortical thickness compared to those who sustained remission, suggesting effects of illness on brain structure. Interpretation: Antipsychotic medication can have deleterious effects on brain structure. Our results, along with reports of increased risk of death, suggest reconsideration of prescribing practice, particularly where alternatives are present. However, potentially adverse effects of relapse on brain structure support antipsychotic treatment during active illness. Trial Registration: Clinicaltrials.gov Registry ID: NCT01427608 Funding Statement: The present study was funded by the NIMH R01MH099167 grant. The STOP-PD II clinical trial from which participants were recruited was funded by USPHS grants MH 62446, MH 62518, MH 62565, and MH 62624 from the National Institute of Mental Health (NIMH). In that trial, Eli Lilly provided olanzapine and matching placebo pills and Pfizer provided sertraline; neither company provided funding for the study Declaration of Interests: A.N. Voineskos receives funding from the National Institute of Mental Health, Canadian Institutes of Health Research, Canada Foundation for Innovation, CAMH Foundation, and the University of Toronto. B.H. Mulsant has received: research funding from Brain Canada, the CAMH Foundation, the Canadian Institutes of Health Research, and the US National Institutes of Health (NIH); research support from Bristol-Myers Squibb (medications for a NIH-funded clinical trial), Eli-Lilly (medications for a NIH-funded clinical trial), Pfizer (medications for a NIH-funded clinical trial), Capital Solution Design LLC (software used in a study funded by CAMH Foundation), and HAPPYneuron (software used in a study funded by Brain Canada). He directly own stocks of General Electric (less than $5,000). E. Dickie receives grant support from the Brain and Behavior Research Foundation N. Neufeld receives grant support from the Physicians’ Services Incorporated Foundation and the University of Toronto A.J. Rothschild has received grant or research support from Allergan, Janssen, the National Institute of Mental Health, Takeda, Eli-Lilly (medications for a NIH-funded clinical trial), Pfizer (medications for a NIH-funded clinical trial), and the Irving S. and Betty Brudnick Endowed Chair in Psychiatry, is a consultant to Alkermes, GlaxoSmithKline, Sage Therapeutics, and Sanofi-Aventis, and has received royalties for the Rothschild Scale for Antidepressant Tachyphylaxis (RSAT)®; Clinical Manual for the Diagnosis and Treatment of Psychotic Depression, American Psychiatric Press, 2009; The Evidence-Based Guide to Antipsychotic Medications, American Psychiatric Press, 2010; The Evidence-Based Guide to Antidepressant Medications, American Psychiatric Press, 2012, and UpToDate®. E.M. Whyte receives grant support from the NIMH and HRSA. B.S. Meyers received research support from the NIMH at the time this work was done. G.S. Alexopoulos has received NIMH grants and has served in the speakers bureau of Takeda, Lundbeck, Otsuka, Alergan, Astra/Zeneca, Sunovion. M.J. Hoptman has received NIMH grants during the conduct of this study. J. Lerch receives grant support from CIHR and the Ontario Brain Institute. A.J. Flint has received grant support from the U.S. National Institutes of Health, the PatientCentered Outcomes Research Institute, the Canadian Institutes of Health Research, Brain Canada, the Ontario Brain Institute, and Alzheimer’s Association. Ethics Approval Statement: Using procedures approved by local institutional review boards, written informed consent was obtained from all participants or their substitute decision maker prior to the initiation of any research procedures.