Objective: Schizophrenia is a devastating mental disorder accompanied by aberrant structural brain connectivity. The question whether schizophrenia is a progressive brain disorder is yet to be resolved. Thus, it is not clear when these structural alterations occur and how they develop over time. Methods: In our selective review, we summarized recent findings from longitudinal magnetic resonance imaging studies investigating structural brain alterations and its impact on clinical outcome at different stages of the illness: (1) subjects at ultra-high risk of developing psychosis, (2) patients with a first episode psychosis, and (3) chronically ill patients. Moreover, we reviewed studies examining the longitudinal effects of medication on brain structure in patients with schizophrenia. Results: (1) Studies from pre-clinical stages to conversion showed a more pronounced cortical gray matter loss (i.e. superior temporal and inferior frontal regions) in those individuals who later made transition to psychosis. (2) Studies investigating patients with a first episode psychosis revealed a decline in multiple gray matter regions (i.e. frontal regions and thalamus) over time as well as progressive cortical thinning in the superior and inferior frontal cortex. (3) Studies focusing on patients with chronic schizophrenia showed that gray matter decreased to a greater extent (i.e. frontal and temporal areas, thalamus, and cingulate cortices)—especially in poor-outcome patients. Very few studies reported effects on white matter microstructure in the longitudinal course of the illness. Conclusion: There is adequate evidence to suggest that schizophrenia is associated with progressive gray matter abnormalities particularly during the initial stages of illness. However, causal relationships between structural changes and illness course—especially in chronically ill patients—should be interpreted with caution. Findings might be confounded by longer periods of treatment and higher doses of antipsychotics or epiphenomena related to the illness.