BACKGROUND The aim of this study was to evaluate the presence of allergic intestinal inflammation in infants with food allergy and atopic eczema before and after elimination diet, and to evaluate the use of eosinophil protein X (EPX) and eosinophil cationic protein (ECP) in the monitoring of inflammatory activity. METHODS The study material comprised 25 infants with atopic dermatitis and food allergy. Thirteen healthy infants served as controls. Faecal and serum samples were collected before an elimination diet (on the first visit to the hospital) and approximately 3 months later for the determination of EPX and ECP. RESULTS Before the elimination diet, infants with atopic dermatitis demonstrated markedly higher faecal concentrations of EPX and ECP than healthy controls (P = 0. 0003, P < 0.0001, respectively). The faecal concentrations of EPX and ECP showed a distinct decrease as a result of an adequate elimination diet in patients with favourable clinical response (P = 0.0027, P = 0.004, respectively). CONCLUSIONS The results indicate the presence of marked intestinal inflammation in patients with atopic dermatitis and food allergy. The determination of faecal ECP and especially of faecal EPX provides a promising noninvasive tool in monitoring intestinal inflammation and disease activity in infants with atopic eczema and food allergy.