In the research studies conducted for the analysis and classification of breast tumors, DNA microassays and gene expression patterns are primarily used. Breast tumors are divided into different groups with these methods. Gene expression-based classifications are known to have important effects on survival and prognosis. Breast cancer is a heterogeneous disease comprised of different histologic subtypes. This heterogeneity results in different clinical presentations and carries different underlying molecular markers. Determining the classification of the tumor based on genomic as well as phenotypic variability will provide important information about the course of the disease and facilitate determining the most relevant therapy model. In this chapter, molecular and genetic factors determining the classification of breast cancer, genomic structure of breast cancer, genetic tests, as well as the role of the developmental hierarchy of the breast epithelial cells and breast cancer stem cells (CSC) on classification will be discussed. © Springer Science+Business Media New York 2013.