Several reports in the literature suggest that many of the phenotypic defects of LPS-hyporesponsive C3H/HeJ mice may be attributed to decreased IFN production by their macrophages. The physical proximity on chromosome 4 of the gene which encodes sensitivity to LPS (Lps) and the structural gene cluster which encodes IFN-alpha (Ifa), suggests the possibility that the Lps gene, whose product is unknown, may actually be a part of the Ifa gene cluster. The C57BL/6J and C3H/HeJ mouse strains carry distinct alleles at both the LPs and the Ifa loci. In this study, we have analyzed these parental strains, as well as 12 recombinant inbred strains derived from these parental strains (e.g., BXH strains), for inheritance of these distinct alleles. The results show the segregation of these two loci: in 5 of 12 BXH RI strains, the IFN-alpha restriction fragment length polymorphism characteristic of one parental strain was discordant with the predicted LPS response phenotype. Therefore, we conclude that the Lps and the Ifa genes are physically distinct despite the apparent cause and effect relationship which is observed phenotypically.