Embryonic stem (ES) cells are pluripotent cells that differentiate into all cell types of the organism. In adult, multipotent tissue-specific stem cells undergo multi-lineage differentiation to preserve normal tissue homeostasis and repair potential injuries. The maintenance of stem cells and their differentiation follows defined epigenetic programs, including DNA methylation, histone modifications and small non-coding RNAs that result in gene expression, morphologic and functional changes. Recently, we reported for the first time the comprehensive characterization of the in vivo gene expression and DNA methylation profiles of four distinct populations of normal human mammary epithelial cells and the identification of cell type-specific DNA methylation patterns with clinical relevance. Our results together with other studies suggest an important role for epigenetic regulation in stem cell self-renewal, pluripotency and differentiation, and imply that abnormalities in these processes may play a role in tumor initiation and progression.