Abstract Gene polymorphism has been found to be associated with the susceptibility to cancer or its severity as exemplified in the CDKN2A gene. CDKN2A regulates G1 arrest and plays an important role in head and neck cancer (HNSCC) carcinogenesis. Deregulated tumor expression of CDKN2A has previously been described in association with HNSCC clinical progression. Aberrant methylation of CDKN2A is common gene silencing mechanism in HNSCC. CDKN2A is polymorphic, with variant alleles G/A442, C/T 540, and C/G 500 associated with cancer. Previously we have shown that in the Puerto Rican population the G/A 442, GG variant is associated with an increased head and neck cancer risk (OR, 4.09). In the present study, we examined the CDKN2A G/A442, C/T 540 and C/G 500 polymorphisms using PCR-RFLP and the pattern of methylation of the CDKN2A gene by methylation-specific PCR or Methylight assay in 152 HNSCC. The allelic frequencies were compared to a control group of 69 age - matched healthy blood donors. CpG island methylation for CDKN2A was found in 45% HNSCCs. The G/A 442, GG variant was more common in tumors of the larynx (63%). A significant correlation between CDKN2A G/A442 and head and neck cancer was indicated (r = 0.24, P = 0.02). We found no association between CDKN2A gene hypermethylation and CDKN2A C/T 540 and C/G 500 polymorphisms, However, we confirmed that individuals carrying the AG variant in G/A 442 gene had a higher frequency of hypermethylation in HNSCCs. Our results suggest that G/A 442 polymorphisms of CDKN2A gene may affect the methylation status. Functional and bioinformatic studies to clarify these results are underway. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2839.