Smoking is a well-known risk factor for Crohn’s disease (CD) onset and aggressive disease course in the Western population. However, previous studies imply that smoking was not associated with an increased risk for CD onset in Asian populations. Therefore, we examined the effect of smoking on the disease course after surgery in Japanese CD patients. Furthermore, we investigated the association between smoking and paneth cell (PC) phenotype, which was recently recognized as a useful biomarker for the disease course of CD.