The intestinal bacterium Enterococcus faecium NCIMB 10415 (E. faecium SF68) has been used for more than a decade as a probiotic strain in animal nutrition as well as in the prevention and treatment of diarrhoea in humans. Beneficial effects have been shown in feeding and clinical trials. However, the strain has no selective growth markers and monitoring in the intestinal tract is impossible by cultivation. Using specific nucleotide sequences, in this study a probe for colony hybridization was constructed in order to quantify this probiotic strain in feed and intestinal and faecal samples from piglets and sows. The probiotic strain showed almost constant amounts in sow faeces (1.8 x 10(5) cfu/g wet weight), while contents in digesta and piglet faeces varied on a lower level depending on gut section and piglet age. The ratio of specific probiotic counts and total enterococci was much lower than in sow faeces however the strain could be detected reliably in faeces already on the 14th day of life. The application of the colony hybridization method enables for the first time the selective detection of the widely used probiotic E. faecium NCIMB 10415 strain among total Enterococcus spp. counts of digesta, faeces and feed. It is now possible to monitor the presence of the probiotic in the intestinal tract and faeces. Results of this study have implications for the proposed modes of action of probiotics in animal nutrition.