BACKGROUND Food allergy is contemplated in atopic eczema. Early recognition of food allergies is difficult and the diagnosis is often missed because of the non-specificity of symptoms. New non-invasive tests are clearly needed. OBJECTIVE AND METHODS We measured the concentrations of tumour necrosis factor-alpha, eosinophil cationic protein and alpha-1 antitrypsin in faeces as indicators of intestinal inflammation induced by double-blind placebo-controlled oral cow's milk challenge in infants and young children with atopic eczema. RESULTS An increased alpha-1 antitrypsin concentration (> 2 mg/g) after cow's milk challenge was detected in 43% of the infants positive as compared with 11% of the infants negative to challenge, P = 0.02. The concentration of eosinophil cationic protein in faeces increased after cow's milk challenge in patients positive to challenge (P = 0.02) but not in those negative to challenge (P = 0.79). The concentration of eosinophil cationic protein was enhanced particularly in patients manifesting immediate-type reactions to the cow's milk challenge. The concentration of tumour necrosis factor-alpha increased after cow's milk challenge in patients positive to challenge (P = 0.005) but not in those negative to challenge (P = 0.25). The concentration of tumour necrosis factor-alpha in faeces was enhanced particularly in patients manifesting delayed-type reactions to the cow's milk challenge. CONCLUSION We conclude that in children with atopic eczema food allergy is associated with intestinal inflammation indicating that more general immunologic disturbances than previously thought take place in these patients. We further suggest that faecal eosinophil cationic protein, tumour necrosis factor-alpha and alpha-1 antitrypsin distinctly indicate various reaction types of food allergy. Parallel testing with eosinophil cationic protein and tumour necrosis factor-alpha may significantly enhance the accuracy in diagnosis of food allergy in patients with atopic eczema.