Borderline personality disorder is characterized by challenges in interpersonal relationships and self-image, impulsivity, and affective instability. Putative neurobiological mechanisms have deepened understanding of the pathophysiology of the disorder, yet challenges remain in the provision of effective treatment. Psychotherapy is the first-line treatment for BPD and though a range of evidence-based modalities are supported, rates of nonresponse are approximately 50%. One approach to improving treatment outcomes concerns research at the cross-disciplinary intersection of neurobiology and psychotherapy. A comprehensive overview of psychotherapy studies that have incorporated biological markers will be provided in this chapter, including neuroimaging, genetics, and neuroendocrine studies. Most studies have investigated task-related brain activation, mainly using affective paradigms that have implicated primarily frontotemporal and limbic regions. High between-study heterogeneity and an overall small number of studies, particularly genetics and neuroendocrine studies, preclude firm conclusions. Recent developments in the field and recommendations for future progress will be discussed.