Borderline personality disorder (BPD) is characterized by enduring psychological distress and affective dysregulation. Several models have linked both phenomena, but are lacking empirical support. To investigate the relation between psychological distress and components of affective dysregulation (especially inability to label emotions, conflictive emotions, and physiological hyperarousal), we repeatedly assessed these components using a 24-hour ambulatory monitoring approach in a group of 50 BPD patients and 50 healthy controls. Hierarchical linear model analyses identified a clear relation between inability to label emotions and distress in the BPD group (p = 0.0009) but not across all subjects (p = 0.6492). Conflictive emotions were related to psychological distress in both groups (p < 0.0001). This relation is, however, most pertinent to the BPD group who experienced conflicting emotions more frequently. Physiological arousal (heart rate) was related to distress in both groups. Our empirical findings emphasize training in labeling emotions and distress tolerance interventions in treatment for BPD.