Regulation of complement activation is essential in the prevention of damage to autologous tissue. This activity is mediated by the presence of specific complement regulatory proteins on the surface of host cells. In humans, one molecule involved in this regulation is a 70-kDa glycoprotein that has been designated decay-accelerating factor (DAF). We present the full-length cDNA sequence and chromosomal localization of the mouse genetic homologue of the human DAF gene. Interestingly, two classes of cDNA clones were obtained that, rather than representing alternately spliced mRNAs, were derived from two separate but closely related linked genes. Both genes encoded proteins with an amino-terminal signal sequence, followed by four short consensus repeats and a domain rich in serine and threonine. Hydrophilicity plots and alignment with human DAF predicted that one gene encoded a glycosylphosphatidylinositol-anchored form of mouse Daf with 64% nucleotide and 47% amino acid identity to human DAF. The product encoded by the second gene was predicted to have an alternate amino-terminal signal sequence and carboxyl-terminal membrane-spanning and cytoplasmic domains. The two mouse Daf genes share 85% nucleotide and 78% amino acid identities, and have been designated Daf-glycosylphosphatidylinositol and Daf-transmembrane to reflect the two alternate mechanisms of membrane attachment. mRNA expression analysis indicated that the two mouse Daf genes were differentially expressed in the adult mouse. Chromosome localization studies mapped the mouse Daf genes to chromosome 1, where they segregated with the C4-binding protein (C4bp) gene.