Abstract Introduction Extracorporeal stool transport (recycling of chyme discharged from the proximal stoma end to the distal end of a high jejunostomy or ileostomy) is thought to be beneficial in preventing malabsoprtion, sodium loss, cholestasis and atrophy of the distal intestine until restoration of the intestinal continuity becomes possible. However little is known about its adverse effects. Our aim was to investigate the microbiological safety of recycling. Material and Method Native samples were taken from the proximal stoma in 5 premature neonates who underwent an ileostomy or a jejunostomy due to necrotising enterocolitis, for qualitative culture. The first sample was drawn immediately after the change of the stoma bag, further samples were sent from the stoma bag at 30, 60, 90, 120, 150, and 180min later. The samples were inoculated by calibrated (10μl) loops onto blood agar (5% sheep blood), eosin–methylene blue agar and anaerobic blood agar, respectively (Oxoid). The aerobic plates were incubated for 18–20h at 5% CO2, whereas the anaerobic plates were incubated for 24–48h in an anaerobic chamber (Concept 400). The bacterial strains were identified to species level by specific biochemical reactions, RapID-ANA II system (Oxoid) and ID32E, Rapid ID 32 Strep ATB automatic system cards (bioMérieux). Results The number of colony forming unit (CFU) of Gram-negative bacteria (mainly E. coli) exponentially increased after 30min and reached 105/ml after 120min. Gram-positive strains (primarily E. faecalis) were detected after 60min and CFU increased to 105/ml after 120min. The number of anaerobic (principally Bacteroides fragilis) CFU started to increase after 120min. In two cases coagulase negative Staphylococcus strains were isolated the earliest in the chyme. The average of total CFU approached 105/ml after 90min and exceeded 105/ml after 120min. Conclusion The chyme in the stoma bag is colonized by commensal facultative pathogenic enteral/colonic as well as skin flora species after 120min. Recycling of stoma bag content may be dangerous after 90min.