PurposeWe examined the clinicopathological characteristics and prognosis of patients with cancer associated with Crohn’s disease (CD).MethodsThe subjects of this study were patients with cancer confirmed in a resected specimen of bowel, who were treated at our institution between September, 1974 and December, 2014.ResultsWe analyzed 34 patients (26 men, 8 women, median age at cancer diagnosis 43.5 years, duration of illness 18 years) and found that the number of those with CD complicated with cancer began to drastically increase after 2005. The site of onset of cancer was in an anorectal lesion in 24 (70.6 %) patients. In 17 (50 %) patients, the cancer was diagnosed before surgery; in 3 patients (8.8 %), it was based on pathological findings during surgery; and in 14 patients (41.2 %), it was based on postoperative pathological findings. Mucinous carcinoma was the dominant histological type, seen in 15 patients (44.1 %), while the special type of signet-ring cell carcinoma was found in 4 patients. The cumulative overall 5 year survival rate was 46.2 %.ConclusionIn this group of Japanese CD patients, an anorectal lesion was the most frequent site of origin of cancer. As cancer was diagnosed preoperatively in only 50 % of these patients, the overall prognosis was poor, with a cumulative 5 year survival rate of just 46.2 %.