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Background & aim: Cytotoxic lymphocyte antigen-4 (CTLA-4) plays an important role in inhibition of T cell activation and resulting in prevention of autoimmune disorder such as systemic lupus erythematosus (SLE). The purpose of the present study was to investigate the relationship between AG 49's polymorphisms in exon 1with systemic lupus erythematosus. Methods: The present case-control study was conducted on 180 patients and 304 healthy controls who were matched in age and ethnicity to the similar individual patient. After DNA extraction from blood samples, polymerase chain reaction (PCR) was used to analyze the genotype and allele frequencies of 49AG polymorphism of CTLA-4 gene. The collected Data was analyzed by SPSS software and Chi-square and Fisher’s exact test. Results: The results indicated that AA genotype was found in 67.2% of patients. A significant difference was seen compared to the control group (p = 0.0001). While the AG genotype with a frequency of 49.7% in healthy subjects compared with patients frequency of 27.8% and G allele with a frequency of 9.2% in healthy subjects and 5% in patients were significantly more common (p = 0.0001). Although the A allele in 81.1 % of patients and in 66% of control group were seen but no significant difference observed. Conclusion: The results showed that the AG 49 polymorphism played an important role in the pathogenesis of systemic lupus erythematosus.