In conclusion, there were significant associations between shorter progression-free survival time in patients with HNSCC and FokI T/T genotype as well as A-T-G (Cdx2-FokI-ApaI) haplotype, although the sample size is not large enough to detect significant differences of minor VDR polymorphisms or synergistic effects of the gene-environment and stratification by tumor stage or primary site. Here, VDR is linked to head and neck squamous cell carcinoma.