Analysis of the patterns of gene expression in breast cancer suggests that it is not a single entity, but is comprised of several biologically distinct subtypes with characteristic molecular profiles. These molecular profiles confirm the clinical impression that estrogen receptor (ER)-negative differs from ER-positive, and expands our understanding by identifying breast cancer subtypes, including the basal-like and human epidermal growth factor receptor (HER)2/ER subtypes within the ER-negative subset, and the luminal A and B subtypes within ER-positive disease. The basal-like subtype is characterized by the low expression levels of the ER-related and the HER2-related group of genes, and therefore is often 'triple negative' on clinical assays for these proteins. This review discusses the molecular profiles of breast cancer with a focus on the clinical characteristics of, and treatment options for, the basal-like subtype.