The TLR9 rs352139 polymorphism was significantly associated with increased SLE susceptibility in heterozygous (AG vs. AA, OR = 1.79, 95% CI [1.07–2.99], p =  0.025), homozygous (GG vs. AA, OR = 2.11, 95% CI [1.06–4.19], p =  0.033), dominant (GG+AG vs. AA, OR = 1.86, 95% CI [1.15–3.03], p =  0.012), and allele (G vs. A, OR = 1.49, 95% CI [1.07–2.06], p =  0.017) models. This evidence concerns the gene TLR9 and systemic lupus erythematosus.