Infectious complications remain one of the most significant problem associated with anticancer therapy in oncological patients. Cytotoxic, radiation and antibacterial therapy induce dysbiosis and gastrointestinal mucosal barrier injury. These changes lead to the mucositis, thereby increasing the risk of endogenous microflora translocation with following probable development of severe infectious and inflammatory diseases. In addition, current evidence suggests that there is a relationship between gut microbiome disturbances and post-transplant graft versus host disease development. The article presents the existing paradigms of determining the role of gastrointestinal tract functional condition in cancer patients in order to optimize prevention and antimicrobial treatment approaches.