The first two lineages to differentiate in the mouse embryo are the trophectoderm and primitive endoderm, which give rise to various extraembryonic structures only. Previous work has shown that all derivatives of these two lineages share the property of undermethylation of repetitive DNA sequences, both satellite and dispersed. Here we show that this undermethylation is not a peculiarity of these repetitive elements but is also a feature of structural gene sequences within both lineages. α-Fetoprotein, albumin, and major urinary protein gene sequences all showed extensive undermethylation at MspI restriction sites in extraembryonic lineages, which did not correlate with their expression in these tissues. The same sequences were heavily methylated in embryonic tissues as early as 7.5 days of development. There are, therefore, major global differences in DNA methylation between the earliest cell lineages to be established in the mouse embryo. The significance of these differences for cellular commitment events remains to be elucidated.