We have investigated whether expression of Ly-49C, detected by the mAb SW5E6, is subject to similar regulation by host MHC as is Ly-49A. Ly-49C expression was regulated by host MHC differentially in mice of A/Sn (A) and C57BL/6 (B) origin. Analysis of AXB recombinant inbred strains suggested two loci regulating the expression, one segregating with the NK gene complex and the other with the MHC. In MHC congenic strains, the A form of Ly-49C had a low expression level and was further down-regulated in the presence of the H-2b haplotype (very low). The B form of Ly-49C had a high expression level and was down-regulated in the presence of H-2Kk (medium). To test the hypothesis that the Ly-49C receptor in A/Sn and C57BL/6 mice may be differentially regulated by MHC products because they represent allelic forms, cDNAs for Ly-49C were cloned by reverse-transcriptase PCR from A/Sn and C57BL/6 mouse strains. The Ly-49C sequences from the two strains differed by six nucleotides leading to four predicted amino acid changes. Both cDNAs could be detected by the Ly-49C-specific Ab when expressed in EL-4 cells. Thus, like Ly-49A, Ly-49C expression is regulated by MHC class I molecules. Furthermore, A/Sn and C57BL/6 mice express different forms of Ly-49C that are down-regulated by different MHC class I molecules.