Nasopharyngeal cancer (NPC) is a common disease in the south part of China, and its incidence is increasing in the southwest of China in recent years. Radiation therapy is the main therapeutic method for NPC in China. In this study, genetic changes were assessed in randomly selected nine NPC patients receiving radiation therapy by different genotoxical screening methods, the cytokinesis-block micronucleus test (CB-MNT), the buccal mucosa cell micronucleus test (BMC-MNT), the undivided lymphocyte micronucleus test (UL-MNT), chromosomal aberration (CA) test, the comet assay and the hprt gene mutation test (HPRT). Patients were used as self-control before receiving radiation therapy. Apart from the UL-MNT, all the methods detected genetic damages in NPC patients, though with different sensitivities. CB-MNT is the best biological indicator for evaluating genetic damage induced by radiation therapy in NPC patients; followed by CA and HPRT, while the BMC-MNT is simplest method as a potential biological indicator.