Borderline personality disorder (BPD) presents with symptoms across different domains, whose neurobiology is poorly understood. We applied voxel-based morphometry on high-resolution magnetic resonance imaging scans of 19 female BPD patients and 50 matched female controls. Group comparison showed bilateral orbitofrontal gray matter loss in patients, but no significant changes in the hippocampus. Voxel-wise correlation of gray matter with symptom severity scores from the Borderline Symptom List (BSL-95) showed overall negative correlation in bilateral prefrontal, right inferior temporal/fusiform and occipital cortices, and left thalamus. Significant (negative) correlations with BSL-95 subscores within the patient cohort linked autoaggression to left lateral prefrontal and insular cortices, right inferior temporal/temporal pole, and right orbital cortex; dysthymia/dysphoria to right orbitofrontal cortex; self-perception to left postcentral, bilateral inferior/middle temporal, right orbitofrontal, and occipital cortices. Schema therapy-based Young Schema Questionnaire (YSQ-S2) scores of early maladaptive schemas on emotional deprivation were linked to left medial temporal lobe gray matter reductions. Our results confirm orbitofrontal structural deficits in BPD, while providing a framework and preliminary findings on identifying structural correlates of symptom dimensions in BPD, especially with dorsolateral and orbitofrontal cortices.