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Nasopharyngeal carcinoma (NPC) is an invasive cancer with particularly high incidence in Southern China and Southeast Asia. The study of NPC is greatly hampered by the lack of reliable cell lines due to the loss of EBV genome and HeLa cell contamination. Conditional reprogramming (CR) cell culture technique has been reported for rapid and efficient establishment of patient-derived normal and tumor cell cultures. The purpose of this study was to assess this method to culture NPC patient-derived primary tumor cells. Using CR protocol, we demonstrated that epithelial cells could be efficiently cultured from normal (70%) and cancerous nasopharyngeal (46%) biopsies. However, by comparing with original tumors in terms of mutation and methylation profiles, epithelial cells derived from cancerous biopsy represented non-malignant cells. Further, they exhibited stem-like characteristics based on their cell surface proteins and could differentiate into pseudostratified epithelium in an air-liquid interface culture system. We conclude that CR method is a highly selective and useful method for growing non-malignant nasopharyngeal epithelial cells.