The murine alpha-fetoprotein (AFP) and albumin genes have been cloned from genomic libraries derived from Balb/c DNA. By restriction endonuclease mapping and electron microscopy, we have shown that both genes are organized similarly into 15 coding segments interrupted by 14 intervening sequences. The sizes of the corresponding coding segments in each gene are identical, lending support to the hypothesis that the two genes, were derived from a common ancestral gene. However, no nucleotide homology between coding segments was observed. Both the sizes and the nucleotide sequence of flanking and intervening sequences have diverged significantly as well. Two regions of the AFP gene, 925 base pairs in the 5' flanking DNA and 180 base pairs in the third intervening sequence, hybridized to the same region of DNA in the third intervening sequence of albumin. The 180-base pair homologies within each gene are present in opposite orientation relative to the direction of transcription, and are associated with reiterated DNA. Thus, it is unlikely that they represent true sequence conservation. An examination of the sizes of the coding segments in each gene reveals a thrice repeated domain, consisting of 4 coding segments. We propose that these correspond to the three domains observed in several mammalian albumins, and in murine AFP.