The human epidermal growth factor receptor 2 gene (HER2), located on chromosome 17 at band q21, is overexpressed in 15% to 25% of breast cancers. Amplification of HER2 (which is also known as ERBB2 or NEU) accounts for 90% to 95% of HER2 overexpression. HER2 encodes a tyrosine kinase receptor that functions in the regulation of cell growth and differentiation. HER2 amplification/overexpression is associated with tumor characteristics seen in aggressive disease, and is subsequently associated with a poorer prognosis and decreased disease-free and overall survival. However, it is also associated with an increased response to certain treatment modalities, particularly trastuzumab therapy. Trastuzumab (Herceptin®; Genentech Inc.) has been shown to confer a significant survival benefit for many patients with invasive, HER2-positive tumors. While HER2 status has generally been assessed by either immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH), chromogenic in situ hybridization (CISH) has recently been introduced as a practical alternative.