Sox17 is a HMG‐box transcription factor that has been shown to play important roles in both cardio‐vascular development and endoderm formation. To analyze these processes in greater detail, we have generated a Sox17‐mCherry fusion (SCF) protein by gene targeting in ES cells. SCF reporter mice are homozygous viable and faithfully reflect the endogenous Sox17 protein localization. We report that SCF positive cells constitute a subpopulation in the visceral endoderm before gastrulation and time‐lapse imaging reveals that SCF monitors the nascent definitive endoderm during epithelialization. After gastrulation, SCF marks the mid‐ and hindgut endoderm and vascular endothelial network, which can be imaged during establishment in allantois explant cultures. The SCF reporter is downregulated in the endoderm epithelium and upregulated in endothelial cells of the intestine, lung, and pancreas during organogenesis. In summary, the generation of the Sox17‐mCherry reporter mouse line allows direct visualization of endoderm and vascular development in culture and the mouse embryo. genesis 50:496–505, 2012. © 2011 Wiley Periodicals, Inc.