Borderline personality disorder (BPD) is a chronic and debilitating syndrome associated with considerable morbidity, mortality, and high rates of medical and psychiatric utilization services. Research focusing on finding a biological observable marker for the purpose of monitoring treatment effects has started to draw attention. Recent research has implicated that brain-derived neutrophilic factor (BDNF) might be a natural candidate for a biological correlate of early life stress. The alterations in levels of BDNF or BDNF methylation in BPD patients compared to general population, or pre- and post- psychotherapeutic treatment might indicate the consequence of epigenetic modification associated with stressful experience or suicide, and may later be able to explain the psychopathology or neuro-development of BPD.