Systemic lupus erythematosus (SLE) is a chronic and progressive autoimmune disease in which reactive oxygen species contribute to pathogenesis. We analysed the distribution of manganese superoxide dismutase (MnSOD2) 47C>T (Ala-9Val) functional polymorphic variants within the mitochondrial targeting sequence in SLE patients (n = 102) and controls (n = 199). We did not find significant differences in the distribution of MnSOD2 47C>T polymorphic variants in SLE patients and controls. However, we found that MnSOD2 Val/Val genotype (recessive model) showed a significant association with Raynaud's phenomenon, odds ratio (OR) = 12.000 [95% confidence interval (CI) = 2.315-62.193], p = 0.0015. We also found that the MnSOD2 Val/Val genotype contributes to immunologic manifestations, OR = 2.957 (95% CI = 1.207-7.243), p = 0.0222, and anti-dsDNA antibody presence OR = 3.365 (95% CI = 1.364-8.304), p = 0.0107, in patients. Our observations indicate that MnSOD2 Val/Val variant can be linked to some clinical manifestations in patients with SLE.