Several recent functional and immunofluorescent studies have suggested that abnormal major histocompatibility genes may be expressed in mice homozygous for the autoimmune disease-accelerating lpr (lymphoproliferation) gene. In an effort to establish the molecular basis of the expression of abnormal MHC molecules in these mice, we used MHC class I- and class II-specific cDNAs to probe endonuclease-digested genomic DNA from strains expressing lpr to look for restriction fragment length polymorphisms (RFLPs). The RFLP pattern of MRL/Mp-lpr/lpr (MRL/lpr) DNA, as determined using five restriction enzymes, was identical to that of MRL/MP-+/+ and typical of the H-2k haplotype exhibited by C3H/HeSnJ and AKR/J, which are the two H-2k haplotype strains from which MRL was derived. DNA from C57BL/6-lpr/lpr (B6/lpr) exhibited a pattern similar to C57BL/6, again indicating that the lpr gene did not alter MHC genes, within the limitations of this approach. Because macrophages derived from lpr mice had been specifically reported to express altered MHC haplotypes, DNA was prepared from MRL/lpr peritoneal macrophages and Southern blotting was performed using probes for I-A beta and I-E beta. The patterns observed were typical of H-2k DNA. The data thus indicate that the abnormalities of MHC genes previously observed in lpr mice may be due to the influence of other genes on MHC gene products, but are probably not due to alterations in MHC genes themselves.