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Background Individuals with posttraumatic stress disorder (PTSD) display reduced hippocampus size and impaired cognition. However, studies on individuals with borderline personality disorder (BPD) are rare, and studies on trauma-exposed patients with BPD but without PTSD are lacking. Methods Twenty-four trauma-exposed women with BPD (10 with PTSD and 14 without) and 25 healthy controls underwent 3-dimensional structural magnetic resonance imaging of the amygdala and hippocampus and a clinical and neuropsychological investigation. Results Compared with controls, patients with BPD and PTSD displayed significantly reduced amygdala (34%) and hippocampus (12%) size and significantly impaired cognition. Trauma-exposed patients with BPD but without PTSD also showed significantly reduced amygdala (22%) and hippocampus (11%) size but normal cognition. Amygdala and hippocampus size did not differ significantly between patients with and without PTSD. Limitations The sample sizes of trauma-exposed groups are relatively small. A larger sample size may have revealed statistically significant differences in amygdala size between those with and without PTSD. Conclusion Our results demonstrate strong amygdala size reduction in trauma-exposed patients with BPD with or without PTSD, much exceeding that reported for trauma-exposed individuals without BPD. Our data suggest that BPD is associated with small amygdala size. Furthermore, evidence is increasing that amygdala and hippocampus size reduction is not only due to PTSD, but also to traumatic exposure. peerReviewed