The notion of uncontrollable stress causing reduced hippocampal size remains controversial in the posttraumatic stress disorder literature, because human studies cannot discern the causality of effect. Here, we addressed this issue by using structural magnetic resonance imaging in rats to measure the hippocampus and other brain regions before and after stress. Chronic restraint stress produced approximately 3% reduction in hippocampal volume, which was not observed in control rats. This decrease was not signficantly correlated with baseline hippocampal volume or body weight. Total forebrain volume and the sizes of the other brain regions and adrenal glands were all unaffected by stress. This longitudinal, within-subjects design study provides direct evidence that the hippocampus is differentially vulnerable and sensitive to chronic stress.