Background and AimVery early‐onset inflammatory bowel disease is defined as inflammatory bowel disease diagnosed before 6 years of age. Very early‐onset inflammatory bowel disease has various differential diagnoses, including primary immunodeficiency disorders, and is known to be resistant to conventional treatment. Therefore, global attention is required to manage this challenging condition. We conducted a retrospective epidemiological survey of the number of patients, final diagnosis, and examinations performed to diagnose very early‐onset inflammatory bowel disease in Japan.MethodsA primary questionnaire about the number of very early‐onset bowel disease cases and its diagnosis was administered to 630 pediatric facilities nationwide in Japan. A secondary survey about the examinations performed to achieve diagnosis was sent to the facilities that responded to the first survey.ResultsThe answering rate was 92.2% (581/630 facilities); 81 facilities had 225 very early‐onset bowel disease patients undergoing their care during the past 68 months. Twenty‐six patients (11.6%) were diagnosed with immunodeficiency‐associated inflammatory bowel disease. The answering rate of the secondary survey was 70.4% (57/81 facilities). Colonoscopy, esophagogastroduodenoscopy, and small bowel imaging were performed for 99.4%, 67.5%, and 28.8% of patients, respectively. Genetic analysis was performed for 26.9% (43/160 patients) of patients, and 51.2% (22/43) of patients were diagnosed with immunodeficiency‐associated inflammatory bowel disease.ConclusionsApproximately 40 patients are diagnosed yearly in Japan. Imaging studies, especially for small bowel lesions, can be challenging for this unique group of patients. However, a comprehensive approach including immunological and genetic analyses appears useful for diagnosing immunodeficiency‐associated inflammatory bowel disease.