C4A‐null alleles (C4A*Q0) and hereditary complete C4 deficiency (homozygous C4A*Q0, C4B*Q0) are associated with systemic lupus erythematosus (SLE). Using Southern blot analysis with C4 and 21‐hydroxylase (21‐OH) DNA probes, we studied SLE patients and normal control subjects with or without C4A*Q0, and 2 C4‐deficient SLE patients. A previously reported large C4A,21‐OHA gene deletion associated in normal subjects with the HLA—A1;B8;DR3;C4AQ0 haplotype was detected by the appearance of a new C4 Hind III 8.5‐kb fragment and disappearance of a 3.2‐kb 21‐OH Taq I fragment. In 3 SLE patients with homozygous C4A*Q0 and 15 with heterozygous C4A*Q0, this deletion pattern occurred almost exclusively in association with the HLA—B8;DR3;C4A*Q0 phenotype; the one exception was a black SLE patient. Other C4A*Q0‐bearing HLA phenotypes in white patients and black patients with SLE, and the 2 completely C4‐deficient SLE patients, had normal DNA hybridization to both C4 and 21‐OH probes. The genetic basis for C4‐null alleles in SLE is heterogeneous. A large C4A,21‐OHA deletion occurs mainly on the HLA—B8;DR3;C4AQ0 haplotype in SLE and controls. Other HLA haplotypes bearing C4A*Q0 have normal C4 and 21‐OH genes, as demonstrated by Southern blot analysis.