Dysregulation of apoptosis plays a key role in carcinogenesis. This study was designed to investigate the association of apoptosis-related gene Caspase 8, Caspase 9 and Bcl-2 polymorphisms with papillary thyroid carcinoma (PTC) susceptibility. We undertook a case-control study of 118 patients and 213 controls to investigate the association between Caspase 8 (-652 6 N ins/del), Caspase 9 (-1263 A>G) and Bcl-2 (-938 C>A) polymorphisms and PTC susceptibility by polymerase chain reaction restriction-fragment length polymorphism and DNA sequencing methods. We further analyzed the distribution of genotype frequency, as well as the association of genotype with clinicopathological characteristics. Overall, no statistically significant association was observed in Caspase 8 (-652 6 N ins/del). Nevertheless, Caspase 9 -1263 GG genotype was at increased risk of PTC (P=0.045; odds ratio (OR)=1.12). Furthermore, GG genotype thyroid cancers were significantly more common in older patients than AA or AG genotypes PTC and in cases of advanced pathological stages. However, Bcl-2 -938 AA genotype demonstrated a protective effect in PTCs (P=0.004; OR=0.35). Polymorphism in Caspase 9 (-1263 A>G) was observed to be associated with susceptibility of PTC. However, Bcl-2 (-938 C>A) polymorphism indicated to play a protective role in susceptibility to PTC. Nevertheless, further investigation with a larger sample size is needed to support our results.