Background and Aims: In the treatment of ulcerative colitis (UC), an incremental benefit of achieving histologic healing beyond that of endoscopic mucosal healing has been suggested; persistent histologic inflammation increases the risk of exacerbation and dysplasia. However, identification of persistent histologic inflammation is extremely difficult using conventional endoscopy. Furthermore, the reproducibility of endoscopic disease activity is poor. We developed and evaluated a computer-aided diagnosis (CAD) system to predict persistent histologic inflammation using endocytoscopy (EC; 520-fold ultra-magnifying endoscope). Methods: We evaluated the accuracy of the CAD system using test image sets. First, we retrospectively reviewed the data of 187 patients with UC from whom biopsy samples were obtained after endocytoscopic observation. EC images and biopsy samples of each patient were collected from 6 colorectal segments: cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and rectum. All EC images were tagged with reference to the biopsy sample's histologic activity. For validation samples, 525 validation sets of 525 independent segments were collected from 100 patients, and 12,900 EC images from the remaining 87 patients were used for machine learning to construct CAD. The primary outcome measure was the diagnostic ability of CAD to predict persistent histologic inflammation. Its reproducibility for all test images was also assessed.