Various endoscopic indices (EIs) are available for evaluating the endoscopic features of ulcerative colitis (UC), but those currently used in clinical trials are not uniform and have been reported to vary considerably. The currently available EIs for UC include qualitative indices (Baron, Matts and Blackstone scores), the Rachmilewitz endoscopic index (REI; total sum of scores of four types of severity of mucosal lesions), among others. As each of these indices has its own unique characteristics, the selection of the proper EI has to be taken into account in the design of the clinical trial. Endoscopy is an observer-dependent diagnostic method, and inter-observer and intra-observer variations are often problematic. Among other factors, the reliability of clinical trials might be reduced considerably if inter-observer agreement is too low. To date, however, few analyses have focused on inter-observer variation in EIs for UC. The study reported here was undertaken to analyze inter-observer variations in the Baron score and REI. The κ statistics, an indicator of inter-observer agreement, was fair and not particularly high for either the Baron score (κ = 0.31) or REI (κ = 0.27). Modifications made to the REI (modified into a 4-point scale by the authors of this study), making it similar to the Baron score, resulted in κ statistics of 0.44 (moderate). The REI, designed to evaluate many mucosal abnormalities, seemed to enhance the validity of endoscopic grading of UC. It is desirable that inter-observer variations in various EIs are analyzed properly and reviewed comparatively. We emphasize the necessity of establishing the optimal EI for designing clinical trials of UC.