BACKGROUND Children constitute 20% of patients with inflammatory bowel diseases (IBD). Still there is a search for a perfect marker for this group of patients which would help in the diagnosis of the disease, in determinating its activity and in monitoring the treatment. OBJECTIVE Evaluate the usefulness of the application of calprotectin measurement in stool samples from children with IBD, as a marker of the severity of inflammation. METHODS We analysed 156 patients: 58 with ulcerative colitis (UC), 67 with Crohn's disease (CD), and 31 from the control group. In all patients the concentration of calprotectin in the sample of feces, markers of inflammation and hemoglobin were measured. RESULTS Concentration of calprotectin in feces of patients with IBD was above the normal range in all patients with moderate and severe disease and in the majority with mild disease or in remission, but it was normal in all patients from the control group. CONCLUSIONS Elevated concentration of fecal calprotectin (FC) was observed in the majority of patients with IBD, but in none from the control group. The number of patients with elevated FC concentration increased together with the disease activity. FC concentration was higher in patients with severe and moderate disease activity. FC concentration in patients with IBD was associated with the increase of inflammatory markers and decreased haemoglobin. Percentage of laboratory abnormalities in children with Crohn's disease and perianal changes was higher. FC concentration can be a noninvasive marker of disease activity in IBD.