To define the relationship between inheritance of major histocompatibility complex (MHC) alleles and susceptibility to the development of systemic lupus erythematosus (SLE), we examined the MHC class I, II, and III phenotypes of white SLE patients and characterized the structures of their class III MHC genes, using Southern blotting. Nine of 88 SLE patients (10.2%) were C4A null. As detected by Southern blot analysis, the C4A gene was deleted from both chromosomes in 8 of the 9 C4A-null patients. Deletions affecting only 1 chromosome (heterozygous) were detected in the remaining C4A-null patient and in 34.5% of SLE patients who were not C4A deficient (compared with 12.5% of controls; P less than 0.05). These results indicate that deletion of the C4A gene is a common genetic marker for SLE. Deletions of C4A were observed most commonly as part of the HLA-B8;DR3 extended haplotype, although deletions were also detected in different HLA haplotypes. Because of the critical role of C4A in the processing of immune complexes, deficiency of C4A may, itself, confer susceptibility to the development of SLE.