The objective of this study was to determine whether the polymorphisms of the CTLA-4 exon 1 (+49) and promoter (-318) are associated with susceptibility to systemic lupus erythematosus (SLE) and its clinical features. Polymerase chain reaction of genomic DNA-restriction fragment length polymorphism was used to determine genotypes of the CTLA-4 exon 1 (+49) and promoter (-318) in 80 SLE patients and 86 healthy control subjects. The genotype distribution of the CTLA-4 exon 1 (+49) differed between SLE patients and controls (chi2 = 6.74, 2 degrees of freedom (d.f.), P = 0.03). The CTLA-4 AG genotype occurred more frequently in patients with SLE (46.3% vs 33.7% controls). On the other hand, the CTLA-4 AA genotype as well as the CTLA-4 GG genotype was less frequent among SLE patients than among control subjects (1.3% vs 9.3% and 52.5% vs 57.0%, respectively). The genotype distribution of the CTLA-4 promoter (-318) differed between SLE patients and control subjects (CT, TT, CC; genotypes 27.5%, 0%, 72.5% vs 16.3%, 4.7%, 79.1% controls respectively, chi2 = 6.36, 2 d.f., P = 0.04). However, Fischer's exact or chi2 P-values for each genotypes of the CTLA-4 exon 1 (+49) and promoter (-318) between SLE and control group were > 0.05. Clinically, in the lupus patients there was no significant difference according to the CTLA-4 polymorphisms. In conclusion, no correlation was found between CTLA-4 exon 1 (+49) and promoter (-318) polymorphisms and SLE in our study.