Collagen type XI α1 (COL11A1) gene overexpression has been implicated as a candidate marker of various types of cancers. In this study, we investigated whether coding region single nucleotide polymorphisms (cSNPs) of the COL11A1 gene are associated with papillary thyroid cancer (PTC) in a Korean population. Four cSNPs [rs12731843 (Lys276Asn), rs3753841 (Pro1335Leu), rs1763347 (Gly1516Gly) and rs2229783 (Ile1602Ile)] were genotyped using direct sequencing in 98 PTC patients and 366 control subjects. Logistic regression analysis for each cSNP revealed an association between rs1763347 and PTC in a dominant model [CT/TT vs. CC, p=0.0042, odds ratio (OR)=0.50, 95% confidential interval (CI) 0.31-0.81]. Analysis of allelic frequency showed that the T alleles of rs1763347 and rs2229783 were significantly associated with reduced risk of PTC (p=0.010, OR=0.61, 95% CI 0.42-0.89 in rs1763347; p=0.007, OR=0.62, 95% CI 0.44-0.88 in rs2229783). Additionally, in the analysis of haplotype, the CC haplotype consisting of rs1763347 and rs2229783 was associated with PTC in codominant (p=0.011, OR=1.56, 95% CI 1.11-2.21) and recessive models (p=0.020, OR=1.70, 95% CI 1.09-2.66). The TT haplotype was also associated with PTC in a codominant model (p=0.006, OR=0.58, 95% CI 0.39-0.88). The frequency of the CC haplotype was higher in the PTC patients (0.71) compared to the control subjects (0.61), whereas the frequency of the TT haplotype was lower in the PTC patients (0.20 and 0.30 in PTC patients and control subjects, respectively). The results suggest that the COL11A1 gene may be associated with PTC and, in particular, that the T allele of rs1763347 and rs2229783 may contribute to a reduced risk of PTC.