Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) is an important negative regulator of T-cell responses. CTLA-4 polymorphisms have been confirmed to be associated with several autoimmune diseases such as systemic lupus erythematosus (SLE). We analyzed the role of +49AG polymorphism in exon1 of the CTLA-4 gene in Iranian patients suffering from SLE. A cohort of 180 SLE patients and 304 ethnically and age matched healthy controls were studied. Polymerase chain reaction restriction fragments length polymorphism (PCR-RFLP) was used to analyze the genotype and allele frequencies of these polymorphisms. We found that the AA genotype was significantly higher in SLE patients (67.2% vs. 41.1%, p=0.0001). The AG genotype frequency, on the other hand, was more frequently reported in the controls (49.7% vs. 27.8%, p=0.0001). The GG genotype was also more common in the control group than SLE patients but the difference was not significant (p=0.06). The frequency of G allele was significantly higher in SLE patients: 34% versus 18.9% than in control (p=0.0001). There was no significant correlation between the risk of developing SLE and the individual’s age, parental consanguinity, and family history of SLE. We didn’t observe any significant association between genotype and the clinical features of SLE. We conclude that the +49AG polymorphism of CTLA-4 gene appear to play a significant role in the development SLE in the Iranian patients, but not to be associated with clinical features of SLE.