Purpose PD-1 receptor is a co-signaling molecule with an important role in regulation of T-lymphocyte activity. Correlation between PD-1 gene (PDCD1) polymorphisms and some immune-related diseases has been reported before. In current study, we aimed to investigate the association of PD-1 polymorphisms at positions +7146 G/A (PD-1.3) and +7785 C/T (PD-1.5), as well as the emerged haplotypes with susceptibility to thyroid carcinoma. Methods One hundred five patients with confirmed thyroid cancer and 160 healthy individuals as control group were enrolled. Genotypes were identified using PCR-RFLP and nested PCR-RFLP methods. Results were analyzed by Arlequin and SPSS software packages. Results Analysis revealed a significant increase in the frequency of PD-1.5 mutant T allele and heterozygous CT genotype in patients with thyroid cancer in comparison with controls [79 (37.7%) vs. 71 (22.2%), and 51 (48.6%) vs. 51 (31.9%), p = 0.0001 and p = 0.009, receptively]. CC genotype at this position observed to be significantly higher among controls than the patients [99 (61.9%) vs. 40 (38.1%), p = 0.0002]. There were no significant differences in the frequencies of genotypes and alleles at locus PD-1.3 between patients and control group. Despite this, GT haplotype emerged from both positions (PD-1.3 G and PD-1.5 T) has also been observed with significant increased frequency between patients and controls [70 (36.8%) vs. 71 (22.2%), p = 0.0005]. Conclusion As the first study to investigate two mentioned polymorphisms in thyroid cancer, current study confirmed the association of PD-1.5 C/T polymorphism and a haplotype resulted from both loci, PD-1.3 and PD-1.5, with susceptibility of Iranians to thyroid cancer.