Non-invasive monitoring of inflammatory bowel disease is an unmet clinical need as patients in clinical remission may have residual mucosal inflammation preceding clinical relapse. We aimed to assess the value of fecal calprotectin and standardized clinical activity scoring to monitor disease activity in ulcerative colitis under medical treatment. Forty-one patients with ulcerative colitis were included in a prospective observational study. Medical treatment was guided by clinical judgement of treating physicians. Fecal calprotectin and the clinical activity index (CAI) were measured blinded to treating physicians every 2 months until the end of follow-up. Twenty-six patients received colonoscopy for clinical reason. As defined by the CAI, patients were in clinical remission (63.4 %), having mild (26.8 %) or moderate (11.2 %) disease activity. Of those in clinical remission (CAI a parts per thousand currency sign 4), 86.4 % showed residual endoscopic activity (Mayo Score a parts per thousand yen1). Calprotectin levels were higher in endoscopically active disease (779.0 vs 331.5 mu g/g, P = 0.034) and calprotectin testing identified more patients with endoscopic disease activity (86.4 %) than the CAI (45.5 %, P = 0.034). Medical treatment was escalated in 90.2 % during the study. Values of the CAI and calprotectin correlated with therapy escalation (OR 3.94 and 3.22, respectively). Only for calprotectin, changes between two measurements were related to intensified medical treatment (OR 1.39). Fecal calprotectin was similarly useful to the CAI to monitor disease activity of ulcerative colitis during medical treatment but identified endoscopic disease activity far more reliably. Changes of calprotectin values between measurements might indicate clinical relapse earlier than the CAI.