Single Nucleotide Polymorphisms (SNPs) are the most common type of genetic variation found in individual’s DNA sequences. SNPs can occur in both coding and non-coding regions of the genome and can affect gene expression, protein function, and disease susceptibility. In this systematic review we evaluate the influence of SNPs as a biomarker in the assessment of oral mucositis (OM) in head and neck cancer (HNC) patients. The study selection process involved screening 66 articles from different platforms, and after removing duplicates and excluding irrelevant articles, 23 articles were included for full-text evaluation. The main characteristics and findings of the selected articles are presented and discussed. We conclude that SNPs can be used as a reliable biomarker for the assessment of OM in HNC patients, and further research is needed to explore the potential of SNPs in personalized medicine for HNC treatment.