Variable number tandem repeat (VNTR) polymorphism located in the 3′ flanking region of the interleukin-6 ( IL-6) gene was examined in Koreans with systemic lupus erythematosus (SLE). We identified 15 VNTR alleles (K1 to K15) in the 3′ flanking region by Genescan analysis. The VNTR K8 allele, a 648-base pair (bp) allele, was most commonly found in Koreans, being present in 74.8% of the SLE patients and 70.3% of the normal controls. The VNTR K9 (642 bp) allele was associated with susceptibility to SLE. In addition, the VNTR K9 was significantly associated with leukopenia ( p = 0.048), thrombocytopenia ( p = 0.020), and elevated C-reactive protein ( p = 0.019). These data suggest that the VNTR K9 in the 3′ flanking region of the IL-6 gene may be associated with disease susceptibility and the clinical phenotypes of SLE.