Objective To compare the role of CTE and CE on the diagnosis of small bowel diseases and evaluate their advantages in patients with different indications.Methods Patients underwent both CTE and CE(interval time <2 weeks)at our institution in recent 3 years were enrolled.The positive detection rates,lesion properties and characteristics of CTE and CE were compared.The diagnostic accuracy of combined method was also analyzed.Results A total of 47 patients were enrolled and the indications included suspected or established Crohn′s disease (28 cases),unexplained abdominal pain (14 cases), obscure gastrointestinal bleeding(3 cases),insufficient small bowel obstruction(1 case)and protein losing enteropathy(1 case).Diagnostic yield of CTE and CE for whole small bowel disorders showed no significant difference(CE 83.0% VS CTE 78.7%,P =0.791).For suspected or established CD,CE had a higher diagnostic accuracy than CTE (78.6% VS 35.7%,P =0.002 ),especially in detecting lesions in the jejunum(CE 50.0% VS CTE 7.1%,P =0.002).The diagnostic accuracy reached 100.0% when two meth-ods were combined.For unexplained abdominal pain,no significant difference was found in the diagnostic ac-curacy of CE and CTE(CTE 42.8% VS CE 50.0%,P =1.000).Diagnostic accuracy of combining CTE and CE was 85.7%.Conclusion CTE and CE are both valuable in detecting small bowel lesions.For pa-tients with suspected or established CD,CE is better than CTE.For patients with unexplained abdominal pain,a combination of CTE and CE may be a better strategy than use CTE or CE alone.