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.