The molecular basis of complement component C4A deficiency in white U.S. and Mexican patients with systemic lupus erythematosus (SLE) was studied. Genomic DNA from SLE patients and non-SLE controls was analyzed for restriction fragments using HindIII and a 5' C4 cDNA probe. C4A gene deletion was recognized by the loss of a 15-kb restriction fragment and the appearance of a 8.5-kb fragment. Thirty-two selected U.S. SLE patients, 7 nonSLE controls, and 11 Mexican SLE patients and 9 relatives were studied. The deletion was recognized in all of the 14 HLA-B8;DR3 SLE patients with a C4A protein deficiency. Two SLE patients with DR3 but without B8 also had this gene deletion. None of the 3 U.S. SLE nonDR3, C4A protein deficient patients nor 20 C4A protein deficient Mexican individuals (11 SLE patients and 9 relatives; none had B8 and/or DR3) showed this deletion. Thus the C4A gene deletion failed to account for the C4A protein deficiency in all the nonDR3 Mexicans and in some U.S. SLE patients. To determine whether gene conversion at the C4A locus would encode a C4B-like protein and be responsible for the C4A protein deficiency (in nonDR3 patients), the C4d region of the gene was amplified by polymerase chain reaction and subjected to Nla IV digestion, and restriction fragment analysis was performed using a C4d region-specific probe. The resulting restriction fragment length polymorphism pattern revealed no changes in the isotype-specific region of the gene as characterized by C4A-specific 276- and 191-bp fragments in Dr3 or nonDR3 individuals. Thus, homoexpression of C4B at both loci was not responsible for C4A deficiency in nonDR3 SLE patients without C4A gene deletion.