The objective of the present study was to determine the effects of the combination of a lactoperoxidase system (LP-s) and lactoferrin (LF) added to a milk replacer diet on severity of diarrhoea, the morphology of the small intestinal mucosa, and the microbiology of digesta and faeces in young calves, in comparison with a control diet. The experiment was conducted with 30 young calves, 15 per treatment, during the period of 7-21 days of age. During this period, calves are sensitive to gastrointestinal disturbances that can cause diarrhoea. The results showed a significantly (p < 0.05) reduced severity of diarrhoea in the LP-s/LF group compared to the control group as assessed by faecal consistency scores. Numbers of CFU (colony forming units) of Escherichia coli in jejunal and colonic digesta and in faeces were lower in the LP-s/LF group compared with the control group. The differences were significant in both colonic digesta (p < 0.1) and in faeces (p < 0.05). Examination of the small intestinal mucosa, using a dissecting microscope, indicated more finger shaped villi in the distal jejunum of LP-s/LF-treated calves compared with the control group (p < 0.05). Histometrical measurements showed that these villi were significantly (p < 0.05) longer.