Background Capsule endoscopy is a relatively new imaging tool for the detection of small bowel pathology. The assessment of the severity of Crohn’s disease by capsule endoscopy is not standardized and is limited by interobserver variations in interpreting the findings. Aim To develop, assess and validate a new, simple capsule endoscopy Crohn’s disease activity index (CECDAI) in order to grade the severity of small bowel capsule endoscopy findings. Methods The system involves dividing the small bowel into proximal and distal segments according to transit time and then rating each segment on the basis of three parameters: inflammation (A), extent of disease (B) and presence of strictures (C). The segmental score is calculated by multiplying the inflammation subscore by the disease-subextent score and adding the stricture subscore (A × B + C); the final score is calculated by adding the two segmental scores: CECDAI = (A1 × B1 + C1) + (A2 × B2 + C2). In the present study, four senior endoscopists (two with experience in capsule endoscopy interpretation) independently reviewed coded capsule endoscopy videos of 20 patients with Crohn’s disease and rated them according to the CECDAI. Interobserver variability was analyzed by Spearman’s correlation test. Results The CECDAI total scores for the 20 patients ranged from 0 to 26. The correlation for the total score assigned between every two observers was 0.867 (0.700−1.000 = strong degree association; WHO classification; P < 0.0001). The Kappa statistics for agreement among all observers for the subscores and total scores were as follows: A1, 0.31 ± 0.05; B1, 0.25 ± 0.05; C1 (no cases); A2, 0.51 ± 0.05; B2, 0.57 ± 0.05; C2, 0.27 ± 0.07. All examiners reported that the system was simple to learn and apply. Conclusions The CECDAI score may serve as a convenient, reliable and reproducible diagnostic and follow-up tool for use by experienced endoscopists in the evaluation of patients with Crohn’s disease of the small bowel.