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The Toll-like receptors (TLRs) are related to innate immunity. TLR9, a member of TLRs, is expressed in immune cell-rich tissues and mediates cellular response. We investigated the association between TLR9 polymorphisms and kidney allograft outcomes. To investigate whether TLR9 polymorphisms are associated with acute rejection after renal transplantation, two single nucleotide polymorphisms (SNPs) of TLR9 gene (rs187084 -1486; rs352140, G2848A) were selected and genotyped by direct sequencing in 342 renal transplant recipients. SNPStats, SNPAnalyzer, Helixtree and Haploview version 4.2 were used to analyse genetic data. Multiple logistic regression models (codominant, dominant, recessive and log-additive) were used to evaluate odds ratios (ORs), 95% confidence intervals (CIs) and P values. Both SNPs, TLR9 rs187084 -1486 and rs352140 G2848A, of recipients were associated with the risk of acute rejection in renal transplantation. C allele of rs187084 -1486 and A allele of rs352140 G2848A were protective genotype for acute rejection (OR 0.6, 95% CI 0.40-0.92; P = 0.018, OR 0.64, 95% CI 0.42-0.98; P = 0.04, respectively). rs187084 -1486 CT and rs352140 G2848A GA genotype were associated with a lower eGFR after a year of renal transplantation. TLR9 polymorphisms, rs187084 and rs352140, of recipients were associated with the risk of acute rejection in renal transplantation. The patients with rs187084 -1486 CT and rs352140 G2848A GA genotype showed a lower eGFR after a year of renal transplantation., (© 2013 John Wiley & Sons Ltd.)