Abstract Food hypersensitivities are becoming increasingly common worldwide. Previous studies indicate that cell mediated immunity has a role in delayed paediatric gastrointestinal food hypersensitivities, but the exact pathogenetic mechanisms are unknown. Cytotoxic activation of T-lymphocytes is known to play an important role in the pathogenesis of celiac disease (CD). The pathogenetic mechanisms of cow's milk protein sensitive enteropathy (CMSE) are largely unknown. CMSE is a non-IgE related type of food hypersensitivity with variable gastrointestinal symptoms but no visible mucosal abnormalities on light microscopy. The diagnosis is based on an open or blinded elimination/challenge test, as the endoscopic, histological and laboratory findings are generally non-specific. This thesis aims to characterize the role of lymphocyte cytotoxicity in the pathogenesis and diagnosis of CMSE in preschool and school aged children, including comparison with CD where the pathogenetic significance of cytotoxicity is well established. The study cohort consisted of 151 children, including 57 with untreated CMSE, 18 with treated CMSE, 24 with CD, and 52 controls. Using immunohistochemistry, the mucosal expressions of cytotoxic T cell-restricted intracellular antigen type 1 (TIA-1), perforin, granzyme A and B were analysed in the duodenal bulb and descending duodenum. Intraepithelial T-lymphocytes were labelled with CD3, alpha/beta and gamma/delta T cell receptor antigens. To determine the rates of overall and epithelial apoptosis as well as proliferation, the immunohistochemical TUNEL technique, M30 and Ki-67 antibodies were used. Serum levels of granzymes, CD30 and soluble Fas were studied using ELISA method. The number of intraepithelial lymphocytes with TIA-1, perforin and granzyme A containing granules was increased in CMSE. This increase was related to antigen challenge and not a constitutional abnormality. The cytotoxic reaction in CMSE differed from that in CD by being of lesser magnitude, concerning predominantly the descending duodenum and not showing signs of cytotoxicity related epithelial destruction. The serum levels of GrA, GrB and CD30 were increased in both CMSE and CD, correlating with the number of duodenal CD3+, alpha/beta and gamma/delta+ intraepithelial lymphocytes. The results strongly support the role of cell-mediated immunity in the pathogenesis of CMSE. Mucosal cytotoxic activation seems to be manifested by the release of cytoxicity related proteins in serum. This provides a new approach to the monitoring of intestinal immune activation which could help in diagnosis and in objectively monitored treatment response.