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In patients with systemic lupus erythematosus (SLE), loss of immunological tolerance to self-nuclear antigens and abnormal activation of self-reactive T and B cells lead to self-antibodies and immune complex production. The autoreactive lymphocytes are removed by the apoptotic process in healthy individuals; however, apoptosis disruption could cause accumulation of apoptotic bodies and nuclear debris. Therefore, apoptosis plays a crucial role in the pathogenesis of autoimmune diseases.To investigate the association between two polymorphisms in an apoptotic-related gene, MDM2, and SLE.A case–control study was conducted on 200 patients with SLE and 206 healthy volunteers matched for age, sex, and ethnicity. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and PCR methods were used for genotyping.No association was found between the MDM2 T309G polymorphism (rs2279744) and SLE. The ID genotype of the insertion/deletion (I/D) polymorphism (rs3730485) was significantly lower in patients with SLE, and the ID genotype could be a protective factor for SLE. The DD genotype was not associated with SLE. The frequency of combined TT/ID and GG/ID genotypes of MDM2 T309G and I/D polymorphisms was lower in the patients with SLE and was associated with a lower risk of SLE. The frequency of the TD haplotype of MDM2 T309G and I/D polymorphisms was significantly lower in patients with SLE and could reduce the SLE risk.The ID genotype of the MDM2 I/D polymorphism was associated with a lower risk of SLE. There was no association between MDM2 T309G polymorphism and SLE.