The procedures most widely used in investigation of intestinal microflora activity are briefly reviewed. The original findings relating to investigation of intestinal microflora and isolation of certain bacterial metabolites from rats with self-filling jejunal loop are presented as an example. Marked correlation between isolation of certain bacterial metabolites and self-filling jejunal loop microflora was observed. The authors consider advisable that biochemical and bacteriological methods for investigation of intestinal microflora be combined. When there are shifts in the number and ratio of the produced metabolites, invasive diagnostic methods including intubation and bacteriological examination of the small intestine are recommended.