This study was conducted to explore the association of endocytoscopy (EC) findings with inflammatory activity and clinical course in ulcerative colitis (UC). EC was conducted for mild to moderate UC 32 cases from January 2010 to August 2016. The EC findings were classified into 4 types: EC-A, regular arrangement of round to oval pits; EC-B, irregular arrangement with/without enlarged spaces between regular pits; EC-C, irregular pits in size and shape with more irregular arrangement of pits; and EC-D, disruptive or disappeared pits. The association of EC classification with Mayo endoscopic grades and clinical activity was examined. A experienced pathologist who was blinded to clinical and endoscopic information evaluated the slices for histopathological assessment of inflammation in UC with special reference to the severity in mucosal inflammatory infiltrates and the presence of crypt abscess and goblet cell depletion. The UC patients who underwent EC were followed up more than 60 months in 22 cases. As a result, there were 15 cases in EC-A, 8 in EC-B, 5 in EC-C and 4 in EC-D. The interobserver agreement was excellent. Each EC-A case was in clinically remission stage, while all the EC-C and EC-D cases were in active stage. In the EC-B group, there were each 4 cases in remission and active stage, respectively. The EC-A cases were divided into Mayo 0 (n=11) and Mayo 1 (n=4), while the EC-B cases were into Mayo 0 (n=2) and Mayo 1 (n=6). There were no cases of Mayo 0 grade in the EC-C and -D group. The EC stratification was significantly associated with the pathognomonic microscopic features. There were significant differences in the percentages of the remission among the EC classifications. None had relapse in the EC-A group during the follow-up period. EC classification could be predictive for relapse in ulcerative colitis. In addition, EC is reliable for assessment of the microscopic inflammatory features.