The definitive endoderm (DE) was first defined as the innermost germ layer found in all metazoan embryos. During development, it gives rise to a vast array of specialized epithelial cell types lining the respiratory and digestive systems, and contributes to associated organs such as thyroid, thymus, lungs, liver, and pancreas. In the adult, the DE provides a protective barrier against the environment and assumes many essential functions including digestion, nutrient absorption, and glucose homeostasis. Since general endoderm formation and patterning have been reviewed recently in a comprehensive manner [1], we will only provide a brief summary of how extracellular signals and downstream transcription factors control endoderm patterning. We will then focus on emerging work addressing the chromatin remodeling events occurring during endoderm organ specification and discuss how these molecular tools can be used to engineer endodermal organs in vitro.