Bowel anisakiasis is rare, and the incidence and clinical features of this condition remain unclear. Using the Japanese Diagnosis Procedure Combination (DPC) in-patient database, we identified 201 cases of bowel anisakiasis between the months of July and December during 2007 and 2008. More than 70% were males. The average age was 54.5 years. Overall, 102 (50.7%) cases had ileus, 16 (8.0%) had perforation or peritonitis, and 4 (2.0%) had intestinal bleeding. Allergic responses, including urticaria, were found in seven (3.5%) patients. Fourteen (7.0%) cases underwent open surgery. Three (1.5%) underwent colonoscopic removal of Anisakis larvae. The average length of stay in the hospital was 9.6 days. The annual incidence of bowel anisakiasis is estimated to be about 3.0 per 1 million people per year. It is important to continue collecting all available data to monitor the trends of this distressing condition.