One hundred and sixty-two unrelated, healthy normals and 118 unrelated SLE patients were subdivided by sex, race, and disease, and each group was in Hardy-Weinberg equilibrium for autosomal codominant expression of the four CR1 alleles. There were no significant phenotypic differences between males and females (P greater than 0.3) or between normals and SLE patients (P greater than 0.2). However, gene frequencies among whites (A:0.87; B:0.12; C:0; D:0.01), blacks (A:0.74; B:0.22; C:0.04; D:0) and orientals (A:0.98; B:0.02; C:0; D:0) were significantly different (P less than 0.05). We had previously reported that SLE patients of phenotype AC had higher relative expression of the C allele than normals and this was confirmed: 61% (SLE, n = 5) vs 22% (normals, n = 3; P = 0.014). Total CR1/E in the AC group (193 in SLE vs 393 in normals 0.05 less than P less than 0.10), was suggestive of the decreased CR1 number seen in larger SLE populations regardless of phenotype. In one large three-generation family with SLE and the C allele, an association between SLE and the C allele is suggested by the presence of the C allele in all three females with SLE versus 3 of 13 healthy females. In informative families in which receptor phenotype and CR1 number/E were determined, it was possible to assign a receptor number to an allele. These data provide evidence for a cis-acting regulatory element that is inherited in association with the CR1 structural gene.