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The reflexive startle- and orienting-response have been widely studied in psychiatric disorders. Existing evidence in patients with borderline personality disorder (BPD) is mixed, and limited to adults. The present study addressed clinical correlates of the psychophysiological orienting response in adolescents with BPD.Female adolescents (13–19 years) with BPD (n = 30), healthy controls (HC; n = 34), and psychiatric clinical controls (CC; n = 53) participated in the trial. Orienting response was induced using acoustic startle-probes (sinus tones) while heart rate (HR) and skin conductance (SCR) were continuously recorded. Besides clinical interviews, the assessment included self-reports on depressive symptoms, anxiety, dissociation and psychopathological distress.On a group level, relative habituation of the HR-response (regression slope) significantly differed between groups (F(2,114) = 3.74, p = 0.027), with significant contrasts (p = 0.026, Sidak corrected) comparing CC (slope 0.04 ± 0.41) and BPD (slope 0.28 ± 0.40). On a dimensional level, relative HR habituation was significantly correlated with the number of BPD diagnostic criteria endorsed (r(117) = 0.183, p = 0.049) and symptoms of dissociation (r(116) = 0.193, p = 0.038), indicating that delayed HR habituation across probes was associated with greater BPD symptom severity. Analyses of SCR showed no significant findings.Findings provide preliminary support for altered habituation of the HR orienting response in adolescent BPD, associated with BPD severity – in particular dissociative experiences. Dissociative experiences may alter the automatic defensive response early in the course of BPD, providing a potential pathway to exaggerated emotional responding in BPD.Alterations of the startle reflex have only been studied in adults with BPD.First study in adolescents with BPD, including healthy and clinical controlsRelative habituation of the HR-response significantly differed between groups.BPD severity and dissociative experiences explained variances on a continuum.Early dissociative experiences may be related to emotion dysregulation in BPD.