The objective of the present study was to determine whether the alterations of cancer predisposition genes were different between radiosensitive and radioresistant patients with Nasopharyngeal Carcinoma (NPC). A total of 21 patients with nasopharyngeal carcinoma were included in this study. All patients were treated with standardized radiotherapy. Sixteen of the tumors were clinically radiosensitive and 5 were radioresistant. Genomic DNA, extracted from Formalin-Fixed Paraffin-Embedded (FFPE) tumor specimens obtained prior to treatment, was subjected to amplicon-based Next-Generation Sequencing (NGS) with primer sets targeting 50 critical human tumor suppressor genes and oncogenes. We identified 18 nonsynonymous mutations, 1 nonframeshift deletion and 1 frameshift mutation distributed across 15 genes, including 11 mutations have been reported in COSMIC (the Catalogue of Somatic Mutations in Cancer) or dbSNP database (database of single nucleotide polymorphisms), and 9 novel mutations. Most of these mutations have not been reported in NPC. More importantly, 5 radiosensitivespecific mutations targeting AKT1, PIK3CA, MET, TP53 and STK11 were observed, suggesting the genetic alterations of PI3K/AKT and p53 pathways were involved in the response to radiotherapy. Collectively, genetic mutations may differentiate tumor radiosensitivity and radioresistance, although validation of such mutations using a large sample size cohort is necessary before a solid conclusion can be reached.