To describe clinical manifestations of patients with interstitial cystitis and bladder pain syndrome (IC/BPS) using a patient registry in Japan. This retrospective cohort study utilized a patient registry supported by the Japanese Ministry of Health, Labor, and Welfare. Patients were classified as IC or BPS based on cystoscopic findings. Data on demographics, comorbidities, symptom severity, pain intensity, and bladder function were collected and we evaluated the differences in clinical characteristics between IC and BPS, and used multivariate analysis to search for additional factors that might contribute to pain. A data set comprising 529 patients was obtained from 14 university hospitals. 66.5% of the cases were classified as IC and 33.5% as BPS. IC patients were significantly aged and female-dominant. Comorbidities such as autoimmune diseases were more prevalent in IC patients. All of the symptom severity, quality of life impairment, and bladder function were significantly worse in patients with IC. Urinary frequency and maximum voided volume on the Frequency-volume chart were 18.8 times and 15.0 times, and 160.9 and 214.1 mL, respectively. Bladder capacity under anesthesia was 293.8 and 472.6 mL, respectively. Maximum voided volume and the number of Hunner lesions were significant predictors of pain in IC patients. The analysis revealed clinical manifestations of IC/BPS using the largest cohort in Japan. The results indicated higher age, higher female proportion, and higher symptomatic and functional severity in IC patients compared to BPS.