An increase in the frequency of methicillin-resistant Staphylococcus aureus (MRSA) as an important causative agent of nosocomial infections is observed worldwide. Unfortunately, in spite of optimal hygienic conditions (barrier isolation, screening, decontamination), patients often remain MRSA positive or are detected as "re-colonized" at readmission. The objective of our study was to clarify if this is due to an undetected colonization of the gastrointestinal tract, which could possibly lead to re-colonization after primary successful decontamination. Therefore, all MRSA strains were collected from 290 in-patients of a university hospital over a period of 2 years. A surprisingly high number (24.1% of all) was isolated from stool samples. Even 13.1% of the total collection could be first observed in this material before detecting MRSA in other materials of these patients. To evaluate the epidemiology of these isolates, pulsed-field gel electrophoresis (PFGE) was used. On the basis of PFGE restriction types one main clone and 11 singular clones could be identified. Additionally, for six individual patients MRSA isolates from stool specimens were indistinguishable from other isolates from different locations. We show here that colonization of the gastrointestinal tract with MRSA apparently could play an important role in spreading MRSA via faecal contamination. Hence, we suggest that stool colonization with MRSA could be the source of a so far unrecognized transmission of MRSA within individual patients and within the population. Therefore, our findings imply a modification in the hygienic strategies for handling decontamination and therapy of MRSA patients.