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AbstractChronic inflammation of the bowel is the characteristic of Inflammatory bowel diseases including Ulcerative colitis and Crohn's disease. The incidence of Inflammatory bowel disease (IBD) in Western Europe is 14/100,000 of inhabitants. Duration and severity of inflammation increases the risk of Colorectal cancer (CRC) development by about 60% in IBD patients. CRC is the 3 rd most common type of tumor in Western population. Every year, more than one million new cases are diagnosed with more than 600,000 deaths.The early detection of CRC, originating from any part of the colon-rectum, is desirable because it can be cured surgically if diagnosed timely. Identification of new early markers for IBD and CRC is very important.This review deals with the searching and identification of possibly new early markers for the above mentioned pathologies. We have focused on intestinal microorganisms (changes in qualitative and quantitative composition of microbiome, selection of candidate microorganisms) and immune system markers (cytokines, chemokines, nuclear factor B, Toll-like receptors andReceptor for Advanced Glycation End Products).