CD19 regulates the signaling for B lymphocyte development, activation and proliferation. In mice, CD19 deficiency and overexpression were shown to result in hypogammaglobulinemia and autoantibody production, respectively. In the present study, we screened for the polymorphisms of CD19, and examined the detected polymorphisms for the association with rheumatoid arthritis (RA), Crohn’s disease and systemic lupus erythematosus (SLE). Two SNPs, c. 705G> T (P235P and IVS14-30C> T, were decreased (P= 0.0096 and P= 0.028, respectively), in SLE. A GT repeat polymorphism, c.* 132 (GT) 12–18, was detected within the 3’-untranslated region, and individuals with⩾ 15 times repeat was significantly increased in the independent two groups of Japanese SLE patients (P= 0.011 and P= 0.035, respectively); the overall difference between total SLE and controls was striking (P= 0.0061). No association was observed for RA and Crohn’s disease. In addition, no variations other than the common polymorphisms were detected in four patients with common variable immunodeficiency, the phenotype of which resembles CD19 deficient mice. In Caucasian SLE families, this GT repeat polymorphism was rare. CD19 mRNA level in the isolated peripheral blood B lymphocytes was lower in individuals possessing (GT) 15–18 alleles compared with those without these alleles, both in controls and in SLE patients; however, the difference did not reach statistical significance. These results suggested that either the slight reduction in the CD19 mRNA level associated with the elongation of GT repeat, or an allele of another locus in linkage disquilibrium with CD19 (GT) 15–18, may be associated with susceptibility to SLE in Japanese.