This study was designed to detect whether nanobacteria (NB) reside in urine and bladder tissue samples of patients with interstitial cystitis/painful bladder syndrome (IC/PBS) and whether antibiotic therapy targeting these organisms is effective in reducing NB levels and IC/PBS symptoms. Twenty-seven IC/PBS patients underwent cystoscopy. Bladder biopsies and urine samples were obtained and cultured for NB, which were identified by indirect immunofluorescent staining and transmission electron microscopy. Eleven bladder samples showed growth of microbes that were identified to be similar to NB. Homologous study of the 16S ribosomal RNA gene suggested that the NB could be the pathogen. For enrolled 11 patients, NB levels decreased dramatically after tetracycline treatment, and they reported significant reduction in the severity of IC/PBS symptoms. A high prevalence of NB was observed in female IC/PBS, and anti-NB treatment effectively improved the symptoms, which suggest that NB may cause some cases of IC/PBS.