Stem cells, with their profound implication in development and enormous potential in regenerative medicine, have been the subject of extensive molecular profiling studies in search of better markers and regulatory schema governing self-renewal versus differentiation. In this review article, we will discuss current advancement in high throughput technologies dedicated to the transcriptome, proteome and genome-wide localization analyses, and how they have been adopted in molecular profiling of stem cells with an emphasis on embryonic stem cell (ESC), hematopoietic stem cell (HSC) and neural stem cell (NSC).