We studied 121 patients with systemic lupus erythematosus (SLE), of whom 119 were complement typed. Both black and white patients with SLE were more likely than racially matched controls to have a C4A null allotype. Patients with homozygous C4A deficiency had less proteinuria than other patients (p = 0.02) and both homozygous and heterozygous C4A-deficient patients (p = 0.05) had fewer seizures than other patients. Anti-dsDNA, anti-Sm, anti-Ro, and anticardiolipin antibodies were less common in patients with homozygous C4A deficiency, with heterozygous C4A-deficient patients intermediate in frequency between homozygous C4A-deficient and normal patients with SLE. Both homozygous and heterozygous C4A-deficient patients (p < 0.005) had higher C3 levels than other patients, and heterozygous C4A-deficient patients had higher, not lower, C4 levels (p < 0.002), compared with non-C4A-deficient patients. C4A gene deletion was found in 23.4% of patients. C4A gene deletion was associated with subacute cutaneous lupus erythematosus (p = 0.04) and Sjögren syndrome (p = 0.02) in patients with SLE. Both anti-dsDNA (p = 0.04) and anticardiolipin (p = 0.04) were found less frequently in patients with C4A gene deletion. Patients with C4A gene deletion had lower C4 levels than patients with C4A deficiency from other mechanisms. We conclude that the presence of 1 or 2 C4A null allotypes and the presence of a C4A gene deletion identify subgroups of patients with SLE that differ in clinical, laboratory, and autoantibody characteristics from other patients with SLE.