The earliest stages of human endoderm development are currently poorly understood. Recent work has shown that mouse endoderm differentiation is mediated by common inductive signals that create distinct lineages [primitive endoderm (PrE) or definitive endoderm (DE)] dependent on developmental context, but whether this same path is followed in humans was unclear. Now, Joshua Brickman and colleagues generate reporter human embryonic stem cell (hESC) lines and analyse their capacity to generate endoderm in vitro. Primed hESCs differentiate to DE in response to Wnt and Nodal signalling, while naïve hESCs do not; rather, they generate PrE. Inhibition of FGF signalling blocks PrE differentiation (consistent with the role of FGF in mouse PrE) and supports naïve hESC self-renewal even in the absence of PKC inhibition. PrE cells derived from naïve hESCs can themselves be cultured as naïve extra-embryonic endoderm (nEnd) when media is supplemented with insulin. These human nEnd cells produce hypoblast-associated basement membrane factors and can be differentiated to a visceral endoderm state by the addition of BMP4. Finally, transcriptomic analysis reveals a correlation between human endoderm in vivo and the authors’ PrE and nEnd cells, which also closely resemble the preimplantation hypoblast in primate embryos. This study thus reveals a conservation of mouse and human endoderm differentiation, and provides powerful tools for comparative lineage studies.