Our results allow for an overview of the distribution of the common HLA alleles in HNSCC patients, uncovering a higher frequency of HLA-A*25 and HLA-C*06 in HNSCC than in a healthy control group and suggesting an association of the HLA-C*04 and HLA-A*02 genotypes with the OS and PFS of patients. Here, HLA-C is linked to head and neck squamous cell carcinoma.