Brain morphologic changes have been reported in borderline personality disorder (BPD), but it remains largely unknown whether BPD is associated with midline brain abnormalities. We used magnetic resonance imaging to investigate the length of the adhesio interthalamica (AI) and cavum septum pellucidum (CSP) as well as third ventricular volume in 20 teenagers with first-presentation BPD and 20 healthy controls. While the CSP length did not differ between the groups, the AI was significantly shorter in BPD patients than in controls. Furthermore, the BPD patients had a significantly larger third ventricle than controls. These preliminary findings suggest that ongoing neuroimaging studies should further evaluate a potential involvement of midline brain structures in the pathogenesis of BPD.