Introduction: Eosinophils contribute to the pathogenesis of inflammatory bowel disease (IBD) in the intestine. Eosinophilic cationic protein (ECP) is one of the most important eosinophilic specific mediators released during activation. The aim of the study was to evaluate the clinical value of serum ECP determination in children with active and inactive IBD and its correlation with disease activity. Material and methods: There were 125 children with IBD (63 with Crohn’s disease - CD, 44 with ulcerative colitis - UC, 18 indeterminate colitis - IC) enrolled in the study. Among them 83 children were in the active phase of the disease, while the remaining 42 were in remission. The control group consisted of 56 healthy children. The ECP was assessed three times in children with active IBD, at baseline and after 2 and 6 weeks of treatment and once in children with inactive IBD and controls using fluoroenzymeimmunoassays. Results: We found elevated ECP at baseline in the total active IBD group when compared to the inactive IBD and control groups, decreasing during treatment. Serum ECP was also elevated in the active UC and CD groups when compared to the inactive UC and CD groups, and correlated with clinical UC and CD activity (R = 0.57 and R = 0.52, p < 0.05, respectively) and duration of the clinical manifestation in UC (R = 0.62, p < 0.05) but not with the disease location in the gastrointestinal tract, or endoscopic and histopathological activity. Conclusions: Evaluation of serum ECP in children with IBD may be useful in disease activity assessment at onset and during the treatment.