Shame and guilt are vital in borderline personality disorder (BPD), and previous research using explicit measures has consistently found elevated levels of these self-conscious emotions (SCE) in those with BPD. However, these measures cannot elucidate implicit processes that are equally important, as they guide the perceptions of the self and influence behavioral responses. Thus, we aimed to extend the research on SCE in BPD utilizing an indirect latency-based measure. A total of 29 female inpatients with BPD and 21 healthy women were assessed with a shame and a guilt self-concept Implicit Association Test (IAT). These two tasks use reaction time measurements to determine the relative strengths of associations between the self versus others and shame versus pride and guilt versus innocence. In addition, participants completed questionnaires capturing shame, guilt, and BPD symptoms. Women with BPD displayed significantly more shame-and guilt-prone implicit self-concepts than the control group (d ϭ 1.2 and d ϭ 0.7, respectively). They also scored significantly higher on explicit measures of shame and guilt. Although explicitly and implicitly assessed shame and guilt were strongly associated with borderline pathology, multivariate models indicated that solely self-reported, but not implicitly measured, guilt was consistently related to all BPD outcomes. Shame was only associated with the number of BPD criteria. This study extends previous findings on SCE in BPD, in that women with BPD do not only explicitly conceive themselves as more shame-and guilt-prone but also exhibit implicitly more shame and guilt self-concepts than healthy controls. Our results may hold clinical and therapeutic implications.