Toll-like receptors (TLRs) are important components of innate immune response. The aim of this study was to investigate whether TLR gene cluster (TLR10-TLR1-TLR6) polymorphisms are associated with the etiology of papillary thyroid carcinoma (PTC) and its clinicopathologic characteristics. We recruited 94 PTC patients and 325 control subjects. Genotypes for each SNP were determined by direct sequencing. SNPStats and SPSS 18.0 were used to evaluate odds ratios (ORs), 95 % confidence intervals (CIs), and P values. Multiple logistic regression analyzes of genetic data were performed. The missense SNP rs11466653 was associated with small tumor size (<1 cm) in PTC. The frequency of the rs11466653 T allele was higher in PTC patients with tumors <1 cm in size than in the control group (95.8 vs. 87.2 %; P = 0.021, OR = 0.30, 95 % CI = 0.11-0.83). The T allele of rs11466653 (T/C, Met326Thr) in TLR10 may be a risk factor for the development of tumors in PTC in the Korean population.