AIM: In order to characterize the qualitative and quantitative microorganisms in different sites of the lower digestive tract (LDT) in healthy volunteers, a specific technique was developed for collecting mucous of the distal ileum, colon and rectum. METHODS: A polyethylene tube was designed to go through the colonoscope channel with a No. 8 French tube. In order to avoid internal contamination, the distal extremity was protected with a membrane of microfilm after being sterilized in ethilene oxid. To facilitate the aspiration of a precise volume, its interior was coated with silicone. One hundred microlliter (0.1 mL) sample of mucous was collected and transferred into an Eppenddorff tube containing nine hundred microlliter (0.9 mL) of VMGA-3 (viable medium of Goteborg). This procedure was repeated at each site of the LDT with a new sterilized catheter. RESULTS: All sites revealed the “non pathogenic” anaerobic bacteria Veillonella sp (average 105 colony forming units/mL-CFU/mL), allowing to conclude an environment of low oxidation-reduction potential (redox) in the LDT. It was also characterized the presence of Klebisiella sp with significant statistical predominance (SSP) in the ileum. Enterobacter sp was found with SSP in the sigmoid colon, Bacteroides sp non-pigmented (npg) and E.coli with SSP in the sigmoid colon and rectum, Enterococcus sp and Lactobacillus sp with SSP in the rectum, all in a mean concentration of 105 CFU/mL. CONCLUSION: This procedure is feasible and efficient and can point out a similar distribution of the aerobic and anaerobic bacteria with the presence of biological markers of normal microbiota in the LDT. AIM: In order to characterize the qualitative and quantitative microorganisms in different sites of the lower digestive tract (LDT) in healthy volunteers, a specific technique was developed for collecting mucous of the distal ileum, colon and rectum. METHODS: A polyethylene tube was designed To facilitate the aspiration of a precise volume, its interior was was through the colonoscope channel with a No. 8 French tube. In order to avoid internal contamination, the distal extremity was protected with a membrane of microfilm after being sterilized in ethilene oxid. coated with silicone. One hundred microliter (0.1 mL) sample of mucous was collected and transferred into an Eppendorf tube containing nine hundred microliter (0.9 mL) of VMGA-3 (viable medium of Goteborg). This procedure was repeated at each site of the LDT with a new sterilized catheter. RESULTS: All sites revealed the “non pathogenic ” anaerobic bacteria Veillonella sp (average 105 colony forming units / mL-CFU / mL), all due to conclude an environment of low oxidation-reduction potential (redox) in the LDT. It was also characterized the presence of Klebisiella sp with significant statistical predominance (SSP) in the ileum. Enterobacter sp was found with SSP in the sigmoid colon, Bacteroides sp non-pigmented (npg) and E. coli with SSP in the sigmoid colon and rectum, Enterococcus sp and Lactobacillus sp with SSP in the rectum, all in a mean concentration of 105 CFU / mL. CONCLUSION: This procedure is feasible and efficient and can point out a similar distribution of the aerobic and anaerobic bacteria with the presence of biological markers of normal microbiota in the LDT.