SOX2 is involved in several cell and developmental processes, including maintenance of embryonic stem cells, differentiation of neural progenitor cells, and patterning of gut endoderm. To study its role in a human system, we generated a human embryonic stem cell (hESC) line harboring a reporter gene encoding GFP in the SOX2 locus. This SOX2 reporter line faithfully recapitulates expression of the SOX2 gene in undifferentiated human pluripotent stem cells (hPSCs), neural progenitor cells (NPCs), and anterior foregut endoderm (AFE). In undifferentiated hESCs, GFP expression corresponds to those cells with highest levels of expression of genes associated with the pluripotent state. In NPCs, expression of GFP can be employed to isolate cells expressing markers associated with NPC multipotency. In AFE, we used transcriptome-wide expression analysis to identify cell surface markers with elevated expression in this population, thereby facilitating isolation and purification of this hPSC-derived cell population.