Objective: Early diagnosis of nasopharyngeal carcinoma (NPC) is an important method to improve the survival rate. However, the sensitivity and specificity of the screening protocols which was widely used in clinic now are considered to be unsatisfactory. Epstein-Barr virus (EBV)-encoded latent membrane protein-1 (LMP-1)is one of the proteins that have been suggested to be a classic oncogene with transformation properties. The current study set out to discuss the clinical significance of LMP-1 on the screening of NPC. Methods: Three hundred patients who visited our institution (Department of Radiation Oncology, Fujian Provincial Cancer Hospital, Fuzhou,China) with ENT symptoms between 2007 and 2008 were involved in this study, and all of them were agreed to be involved in this investigation. Not only did they undergo nasopharyngeal swab to obtain cells for the LMP-1 polymerase chain reaction (PCR) analysis, but also nasopharyngeal biopsy were taken to identify the diagnosis. Results: An amount of DNA that was sufficient for PCR was extracted from 243 (81%) swab samples, the positive rate of LMP-1 of those with non-nasopharyngeal carcinoma was 3.85% (4/108), which was much lower than those with nasopharyngeal carcinoma (P ＜ 0.05). By detecting LMP-1 in nasopharyngeal swabs, NPC was diagnosed with a sensitivity of 88.15% (119 of 135 patients), specificity of 96.30%(104 of 108 patients), a positive predictive value of 95.2% (119 of 123 patients), a negative predictive value of 86.67% (104of 120 patients), accuracy of 91.77%, and Youden index of 84.45%. Conclusion: The nasopharyngeal swab coupled with PCR-based EBV LMP-1 detection have high sensitivity and specificity, and also good repeatability, it could serve as part of the screening program for high-risk populations.