Hippocampal abnormalities may be implicated in the pathophysiology of mental disorders with affective symptoms such as borderline personality disorder (BPD) and bipolar disorder (BD). We aimed to investigate hippocampal morphology in BPD and BD patients, compared to 1:1 age- and sex-matched healthy controls (HC) using a three-dimensional mapping method. Manual tracing of the hippocampi on magnetic resonance imaging (MRI) images was performed on 26 patients with BPD (age: 38±11; sex (f): 16 (61%)) and 15 with BD (age: 44±9; sex (f): 5 (33%)) and their age- and sex-matched HC (for BPD: n=26; age: 38±11; sex (f): 16 (61%); for BD: n=15; age: 44±9; sex (f): 5 (33%)). Compared to their reference groups, BPD patients showed smaller hippocampal volume bilaterally. The BD group showed significantly smaller right hippocampal volumes. In the surface maps, alterations were localized to different hippocampal sectors for the two groups: the CA1 regions and subiculum, bilaterally, in BPD, and the right dentate gyrus in the BD group. These differences persisted after controlling for alcohol and substance abuse. BPD and BD groups may exhibit distinct patterns of volumetric MRI changes in hippocampal subdivisions that might be related to the clinical phenomenology of each disorder.