The human intestine is colonized by a multitude of microbes such as bacteria, viruses, archaea, fungi and other eukaryotes. It is a complex and dynamic ecosystem established during the first years of life. The availability of new sequencing tech-nologies and bioinformatic methods has made it possible to analyze the human microbiome quickly and affordably at the molecular level. These molecular analyses of the 16S-ribosomal RNA have increased previous culture-dependent esti-mates of the total microbiota from 200 to 300 species to up to 1800 genera with up to 36,000 species. Importantly, the microbial composi-tion can be influenced by various factors such as nutrition, stress and medication. Therefore, the exact composition of intestinal micro-biota is as unique as the fingerprint. Inflammatory bowel diseases (IBD), including ulcerative colitis and Crohn’s disease, are chronic and relapsing inflammatory disorders of the intestine. Although their incidence is increasing globally, the precise etiology remains unclear, and a cure for IBD has yet to be discov-ered. The most accepted hypothesis of IBD pathogenesis is that complex interactions between genetics, envi-ronmental factors, the microbiota, and the host immune system lead to aberrant immune responses and chronic intestinal inflammation. Recent studies have shown that a shift in the composition of the microbiome can also be observed in patients with chronic inflamma-tory bowel diseases. In addition, the incidence of intestinal infections has increased over the past 15 years among hospitalized IBD patients, primarily driven by Clostridium difficile infections. Thus, fecal microbial transplantation (FMT) is currently emerging as one of the more promising microbiome-mod-ulating IBD therapies. It cannot be answered in general terms whether the microbiota is friend or foe of IBD; presumably both is true. Pro-spective studies that are focusing on the gut microbial composition, the epithelial integrity and the mucosal immune system in IBD are therefore warranted to shed light on this ques-tion in more detail. Although the large number of scientific publica-tions suggests that our knowledge in this field has exponentially expanded over the past 10 years, research is still in its infancy. Intensive ongoing research in the future will show to what extent we will use the modula-tion of the intestinal microbiota for human health.