The TP53 rs1042522 CC and ATM rs1801516 A, together with T3–4, N > 0 and non-oropharyngeal tumor localization, were independent indicators of poor LRFS, while the XRCC6 rs2267437 CC genotype, HPSCC and regional recurrence after treatment had independent negative effects on MFS. Here, XRCC6 is linked to neoplasm of oropharynx.