An intestinal microflora and its metabolism is the object of interest in number of investigations worldwide. Microflora presents in bowels is suspected to have a role in ethiopathogenesis of inflammatory and neoplasm bowel diseases. The assessment of bacterial fermentation processes in 40 children with inflammatory bowel syndrome (IBS), irritable bowel disease (IBD) and constipation (C) was introduced in paper. The hydrogen breath test (HBT) was used to asses the presence of hydrogen and methane in expired air. The utilisation process of free hydrogen and time of intestinal passage were determined. The prolongation of intestinal passage enhances a development of methane synthetising microflora what was observed in most of the patients with IBD and C. Methanogenesis increases with age undependent to gender. In IBD and IBS with predominating diarrhoea patients the increase of hydrogen was observed in the beginning, then its normalisation occurred with no methanogenesis at all. However the HBT enhanced the clinical symptoms of the disease what can be combined with the development of sulphate-reducing bacteria (SRB). They have affinity to hydrogen, and hydrogene sulpide, the end product of their metabolism is responsible for the occurrence and clinical course of IBD. The obtained results suggests that further research on bowel microflora should be continued.