Microbiota as a predictor of malignant neoplasms of the gastrointestinal tract has been extensively studied in medicine, and an increasing number of research is being devoted to the determination of the bacterial flora of tumors. However, there is an assumption that it is the presence of viral and bacterial agents that play an important role in the development of malignant neoplasms of a particular organ of the digestive system due to changes in the genome of infected cells in viral invasion and the development of an inflammatory reaction in bacterial infections. This literature review describes the role of infectious flora in carcinogenesis in the organs of the gastrointestinal tract, presents promising areas for future research on microbiota in malignant neoplasms of the digestive system, and touches upon the development of new approaches to the administration of immunotherapy to oncological patients. © 2025 Elsevier B.V., All rights reserved.