Breast cancer is a heterogeneous disease, encompassing multiple entities associated with distinct biological features and clinical behaviours. Microarray-based expression profiling analysis has been used to unravel the molecular underpinning of several characteristics of breast cancer, including its proclivity to disseminate to distant sites and the molecular basis of histological grade. Furthermore, a breast cancer molecular classification based on transcriptional analysis has been proposed. However, microarray studies have primarily analysed invasive ductal carcinomas of no special type. Histological special types of breast cancer, which account for up to 25% of all invasive breast cancers, have not been systematically studied. Despite the limited interest, in recent years it has become apparent that the histopathological characteristics of these cancers may be underpinned by distinct arrays of genetic changes, providing direct evidence for genotypic-phenotypic correlations between morphological patterns and molecular changes in breast cancer (eg t(12;15) in secretory carcinoma of the breast). Here we review the molecular characteristics of special types of breast cancer, with special emphasis on their microarray-based expression profiles and their impact on our understanding of breast cancer.