During the process of embryo development, formation of tissues and organs is strongly dependent on the correctly temporal-spatial differentiation and proliferation of stem cells, as well as apoptosis of intermediate cells. The processes of cell fate determination require sophisticated coordination, in order to promise the appropriate morphogenesis of tissues and organs during embryo development. GATA transcription factors play essential roles in this process, for example, in germ layer determination, hematopoietic system and cardiac formation, and also function in the genesis of thymus, intestine and tumor. Based on the current findings and combined with our research, this review will introduce the important function of GATA transcription factors in maintenance and differentiation of stem cells, as well as in cell reprogramming.