Extra-embryonic-specific imprinted expression is restricted to defined lineages in the post-implantation embryo

► Maternal contamination exaggerates imprinted expression in placenta. ► The visceral yolk sac (VYS) endoderm shows widespread imprinted expression. ► New technique to separate VYS reveals masked endoderm imprinted expression. ► Expression of imprinted genes in VYS is regulated by DNA methylation. ► VYS is an improved model for extra-embryonic imprinted expression.