Objective: To find the genes correlated with the metastasis of head and neck squamous cell carcinoma by detecting the specimens of head and neck squamous cell carcinoma. Methods: 80 specimens of head and neck squamous cell carcinoma ，including 17 cases of tongue, 13 cases of oral, 14 cases of oropharynx and 36 cases of hypopharynx, were detected by single nucleotide polymorphism chip.In the follow-up period,as the test group 39 patients occurs distant metastasis,as the control group 41 patients did not occur distant metastasis.Results: The results of single nucleotide polymorphism（SNP） showed a distinct peak of frequent genomic gain at 11q13. Using Cox analysis of the array data, we found relative risk of T allele of rs9651738 as the snp probe of SHANK2 gene was 3.61（P=0.003）, relative risk of T allele of rs4980690 as the snp probe of FGF4 gene was 3.63（P=0.003）, relative risk of T allele of rs7929885 as the snp probe of ANO1 gene was 4.35（P=0.008）, relative risk of T allele of rs687660 as the snp probe of PPFIA1 gene was 4.24(P=0.011) , relative risk of T allele of rs6606651 as the snp probe of ORAOV1 gene was 3.04(P=0.013), relative risk of T allele of rs592412 as the snp probe of CCND1 gene was 4.07(P=0.013). Conclusion: These genes at 11q13 can increase the risk of metastasis of head and neck squamous cell carcinoma and possibly become the therapeutic target.These genes include T allele of rs9651738 in SHANK2, T allele of rs4980690 in FGF4 , T allele of rs7929885 in ANO1 , T allele of rs687660 in PPFIA1 , T allele of rs6606651 in ORAOV1 and T allele of rs592412 in CCND1.