Humans are host to complex microbial communities that were previously termed “normal flora” and largely overlooked. However, it is increasingly understood that resident microbes contribute to both health and disease, including the risk for malignancy. Investigators are just beginning to define microbes, or groups of microbes, that contribute to the development of gastrointestinal malignancies and the mechanisms by which this occurs. Resident microbes can induce inflammation, leading to cell proliferation and altered stem cell dynamics, which can lead to alterations in DNA integrity and immune regulation and thus promote carcinogenesis. Studies in human patients and rodent models of cancer have identified alterations in the microbiota of the stomach, esophagus, and colon that increase the risk for malignancy. Manipulation of the composition and/or function of the gastrointestinal microbiota could allow for the prevention or treatment of certain gastrointestinal malignancies in the future.