Purpose To investigate the pathological characteristics of loco-regional recurrent nasopharyngeal carcinoma ( rNPC ) . Methods Nasopharyngeal biopsy specimens of 46 rNPCs and 63 primary NPCs were collected. HE staining, immunohistochemistry and EBV small RNAs ( EBERs) in-situ hybridization were performed. Results The over-expression rates of both p63 and CK5/6 in rNPC were significantly higher than those of primary NPCs (P=0. 005, P=0. 026), while no statistical significance of Ki-67 over-ex-pression existed between the two groups ( P=0. 387 ) . More necrotic tissues, inflammatory exudates, giant bizarre carcinoma cells, desmoplastic stroma, giant bizarre tumor cells and higher degree of squamous differentiation were found in rNPCs. The carcinoma cells of 5 rNPCs were negative for both EBERs in-situ hybridization and LMP-1 immunohistochemical staining. Conclusion The loco-re-gional rNPC has two peaks of latency interval:2~5 and 9~11 years. The loco-regional rNPC cells have higher degree of squamous differentiation with higher expression of p63 and CK5/6, as well as more invasive ability. In addition, both EBERs in-situ hybridization and LMP-1 immunostaining are negative in 10. 87% (5/46) of loco-regional rNPC.