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The human cytotoxic T lymphocyte antigen-4 (CTLA-4) gene has been confirmed to be associated with several autoimmune diseases. In this study, we investigated the CTLA-4 gene polymorphism in systemic lupus erythematosus (SLE) Egyptian patients. A polymerase chain reaction was conducted to amplify CTLA-4 gene, followed by restriction fragment length polymorphism (RFLP) assay to detect candidate genetic polymorphism at positions -1722 T/C and -1661 A/G. Sixty SLE patients (55 females and 5 males) with mean age 28.5 ± 7 years and 40 healthy controls (31 females and 9 males) with mean age 27.8 ± 6.2 years were included in this study. The genotypic distribution at position -1661 of CTLA-4 gene was GG (11.7 %), AA (70 %), and AG (18.3 %) in SLE patients versus GG (20 %), AA (65 %), and AG (15 %) in the control (
P
value 0.508); regarding the position -1772 of CTLA-4 gene, the distribution was TT (83.3 %) and TC (16.7 %) in SLE patients versus TT (77.5 %) and TC (22.5 %) in the controls (
P
value 0.466). On studying the clinicopathological impact of the studied single nucleotide polymorphism (SNPs) with the disease severity, there is a statistical significance (
P
= 0.011) for the presence of AA genotype and severity of disease at -1661 genotype. AA genotype at -1661 was protective against discoid rash (
P
= 0.005), TC genotype at -1772 site is protective against serositis (
P
= 0.05), and serositis occurs more commonly with the AG genotype at -1661 site (
P
= 0.038). In our study, we concluded that the studied SNPs at positions -1772 and -1661 of CTLA-4 gene were not associated with SLE risk in Egyptian population.