Understanding the biological connections to mental processes was one of the original goals of psychoanalysis, and the development of cognitive and affective neuroscience and its methods might contribute to actualizing this goal. Personality disorders provide an opportunity to examine the complex mental structures of individuals experiencing extreme difficulties in interacting with their social environment. We provide initial information on a collaboration exploring an approach to one of the most serious personality disorders, borderline personality disorder, based upon the study of normal attention, individual differences in temperament, self definition and attachment organization, with the potential to illuminate the psychology and psychobiology of the disorder and to contribute to psychotherapeutic intervention. This developing model of borderline personality disorder can relate the symptoms to more enduring temperamental aspects of the patients. The goal is to understand the development of neural networks that underlie the abnormalities of adults, and eventually work out the interaction between temperament, genes, and experience that produce the disorder, and potentially inform intervention.