Mice deficient for the transcription factor neurogenin 3 (ngn3) fail to develop endocrine cells in the intestine and pancreas and show partial endocrine differentiation in the stomach. We expressed Cre recombinase under control of a ngn3 BAC to achieve high fidelity cell lineage tracing in vivo to determine whether endocrine cells in these organs differentiate from NGN3+ precursor cells. Our results indicate that all small intestinal enteroendocrine cells arise from ngn3-expressing cells and confirm that NGN3+ cells give rise to all pancreatic endocrine cells as noted previously. By examining mice at a developmental stage when all of the cell types in the stomach have differentiated, we have delineated region-associated differences in endocrine differentiation. A much smaller fraction of endocrine cells populating the acid-producing region of the stomach is derived from NGN3+ precursor in contrast to the antral–pyloric region. Unexpectedly, ngn3 is expressed in cells that adopt non-endocrine cell fates including significant fractions of goblet and Paneth cells in the intestine and a small number of duct and acinar cells in the pancreas. Rarely, ngn3 was expressed in pluripotent cells in intestinal crypts with resultant labeling of an entire crypt–villus unit. Thus, ngn3 expression occurs in mixed populations of immature cells that are not irreversibly committed to endocrine differentiation.