Amplification or over-expression of the HER2/neu receptor is present in 20-30% of invasive breast cancers and in 60% of intraductal breast carcinomas. Patients with HER2/neu gene aberrations have more aggressive disease, frequent disease recurrence and a shorter survival. Trastuzumab (herceptin) is a monoclonal antibody selectively directed against the HER2/neu receptor. The addition of trastuzumab to chemotherapy in HER2/neu-positive advanced breast cancer patients has increased complete and partial response rates, and prolonged time to progression and overall survival. However, a relatively common failure site in patients administered trastuzumab is the central nervous system (CNS). CNS metastases in these patients seem to develop despite responses achieved in extracerebral sites. This pattern of failure has mainly been attributed to the lack of trastuzumab penetration to the CNS owing to the high molecular weight (145 kDa) of this molecule. Additionally, increased risk of CNS relapse may be associated with improved systemic control of extracerebral metastases and prolonged survival without brain protection (a sanctuary site). Finally, it was postulated that HER2/neu over-expression and/or amplification might predispose to brain metastases. The aim of this article is to discuss the pathophysiology of this phenomenon and its clinical implications.