Cattle are the only non-primate species to have an expanded KIR gene family. In addition they have a single Ly49 gene, thought to be monomorphic. We have identified two additional Ly49 cDNA sequences in cattle that encode molecules predicted to differ by 14 and 16 amino acids from the original sequence. All available data indicate the presence of only one Ly49 gene in cattle, thus the divergent sequences reported here may represent ancient allelic lineages, a high level of polymorphism in an ancestral gene or a previously expanded and subsequently contracted Ly49 gene family. Cattle are the only species known to have an expanded polymorphic KIR gene family and a polymorphic Ly49 gene.