Interstitial cystitis/bladder pain syndrome with Hunner's lesion (HIC) is characterized by chronic inflammation and nerve hyperplasia; however, the pathogenesis of HIC remains a mystery. In this study, we detected both EBV latency infection genes EBNA-1, LMP-1, and EBV lytic infection BZLF-1 and BRLF-1 expression in the HIC bladders, indicating coexistence of EBV persistence and reactivation in the B cells in HIC bladders.