Neuroimaging studies have identified patterns of brain abnormalities in various stages of schizophrenia, but whether these abnormalities reflect primary factors associated with the causes of illness or secondary phenomena such as medications has been unclear. Recent work conducted within the prodromal risk paradigm suggests that progressive change in brain structure and function occurs around the time when clinically high-risk individuals transition into full-blown psychosis, effects that cannot be explained by exposure to medications or illness chronicity. This article reviews recent work bearing on the question of the timing of onset and course of brain changes, focusing on structural MRI, diffusion tensor imaging, and resting state connectivity MRI, in association with the onset and course of psychosis. We conclude with a consideration of potential mechanisms underlying progressive tissue changes during the prodromal phase of schizophrenia and implications for prevention.