Breast cancer is a complex and heterogeneous disease, comprising multiple tumor entities associated with distinctive histological patterns and different biological features and clinical behaviors. Microarray-based high-throughput technologies have been employed to unravel the molecular characteristics of breast cancer, including its proclivity to disseminate to distant sites, and the molecular basis for histological grade. In addition, a breast cancer molecular taxonomy based solely on transcriptomic analysis has been proposed. Most microarray studies have focused on invasive ductal carcinomas of no special type, neglecting the important information about the biology and clinical behavior of breast cancers conveyed by histological type. Histological special types of breast cancer account for up to 25% of all invasive breast cancers. The histopathological characteristics of these cancers might be driven by specific genetic alterations, providing direct evidence for genotypic-phenotypic correlations between morphological patterns and molecular changes in breast cancer. We review the historical aspects of breast cancer taxonomy, discuss the possible origins of the diversity of breast cancer and propose an approach for the identification of novel therapeutic targets on the basis of histological special types of breast cancer.