OBJECTIVE In an effort to establish whether a 28 base pair (bp) deletion in the gene for the 2nd component of complement (C2) constitutes a significant genetic risk factor for systemic lupus erythematosus (SLE), we determined the frequency of this mutation in SLE and control populations. The MHC associations of this mutation were also established. METHODS Polymerase chain reaction (PCR) was used to amplify DNA, and the wild type and mutant alleles were distinguished by gel electrophoresis. RESULTS Among 122 Caucasoid patients with SLE, 2 homozygous and 2 heterozygous carriers of the 28 bp deletion were found, giving a gene frequency of 0.0246. In contrast, 6 of 427 North American Caucasoid controls were heterozygous for the 28 bp deletion, giving a gene frequency of 0.0070 (p < 0.05). Carriers of the 28 bp deletion in C2 frequently carried the DRB1*1501 allele. The 28 bp deletion in C2 was not found in 194 African-American controls or in 127 African-American patients with SLE. CONCLUSIONS A direct assay for the most common form of C2 deficiency established that the 28 bp deletion in the C2 gene is significantly more common in Caucasoid patients with SLE compared to controls (p < 0.05). When only heterozygous carriers of the 28 bp deletion were enumerated, they were not found more frequently in the Caucasoid population with SLE compared to controls.