Mouse embryos homozygous for the mutation embryonic ectoderm development (eed) exhibit a growth defect and fail to gastrulate normally. While extraembryonic mesoderm is produced extensively, very little embryonic mesoderm is detected in eed mutant embryos, and there is no subsequent organization of mesoderm into node, notochord, or somites. The phenotype is consistent with a defect in the distal primitive streak. Here we report additional phenotypic analyses that include mRNA in situ hybridization of genes whose expression reflects the function of different regions of the primitive streak and their derivatives. These studies have confirmed that mesoderm derived from the proximal primitive streak is specified appropriately. Despite the absence of a morphologically distinct node, sparse axial mesoderm cells in eed mutant embryos are specified, as reflected by expression of Brachyury (T), Sonic hedgehog, and Tcf3b/HNF-3 beta, and definitive endoderm is produced. Specification of these cell types is also independent of correct expression of nodal, Fgf4, and gsc. Finally, T and Evx1 display ectopic expression in cells not normally fated to ingress through the primitive streak. The data presented are discussed in terms of mechanisms for establishment of the eed phenotype, and are consistent with the eed gene product playing an early role in primitive streak formation and/or organization.