Differentiation of small bowel tuberculosis (SBTB) from Crohn's disease (CD) is a diagnostic challenge. We studied 52 patients with suspected SBTB or CD with terminal ileal involvement, who were prospectively enrolled. After confirming patency of the gastrointestinal tract, 26 patients underwent capsule endoscopy (CE). A final diagnosis of CD was found in 18 patients and SBTB in eight patients. All SBTB patients had involvment of the ileocecal valve (ICV) with large (n=6) and aphthous (n=2) ulcers in the ileal segment. In CD, ICV involvement was seen in five (33%) patients. Large and aphthous ulcers were observed in seven (47%) and 15 (100%) patients, respectively. On comparison with CD, patients with SBTB had increased frequency of ICV involvement (P=0.002) and lesser frequency of aphthous ulcers (P=0.007). CE can help in differentiating CD from SBTB by the position of its involvement and the type of ulcers present.