High wavenumber (HW) Raman spectroscopy has weaker fluorescence background compared with fingerprint (FP) region. This study aims to evaluate the discrimination feasibility of nasopharyngeal non-cancerous and nasopharyngeal cancer (NPC) tissue with both FP and HW Raman spectroscopy. HW Raman spectra of nasopharyngeal tissue were obtained for the first time. Raman spectra were collected to differentiate nasopharyngeal non-cancerous (n = 37) from NPC (n = 41) tissues in FP (800–1800cm−1), HW (2700–3100cm−1), and integrated FP/HW region. First, to assess the utility of this method, the averaged Raman spectral intensities and intensity ratios of corresponding Raman bands were analyzed in HW and FP regions, respectively. The results show that intensities as well as the ratios of specific Raman peaks might be helpful in distinguishing nasopharyngeal non-cancerous from NPC tissue with the HW Raman spectroscopy, as with FP Raman reported before. The multivariate statistical method based on the combination of principal component analysis–liner discriminant analysis (PCA-LDA), together with leave-one-patient-out, cross-validation diagnostic algorithm, was used for discriminating nasopharyngeal non-cancerous from NPC tissue, generating sensitivities of 87.8%, 85.4%, and 95.1% and specificities of 86.5%, 91.9%, and 89.2%, respectively, with Raman spectroscopy in the FP, HW, and integrated FP/HW regions. The posterior probability of classification results and receiver operating characteristic curves were utilized to evaluate the discrimination of PCA-LDA algorithm, verifying that HW Raman spectroscopy has a positive effect on the differentiation for the diagnosis of NPC tissue by integrated FP/HW Raman spectroscopy. What's more, the potential of Raman spectroscopy used for differentiating different pathology NPC tissues was also discussed. The results demonstrate that both FP and HW Raman spectroscopy have the potential for diagnosis and detection in early nasopharyngeal carcinoma, and HW Raman spectroscopy may improve the discrimination of NPC tissue compared with FP region alone, providing a promising diagnostic tool for the diagnosis of NPC tissue. Copyright © 2015 John Wiley & Sons, Ltd.