The term “Gastro-Intestinal (GI) cancer” indicates a group of tumors that affect the digestive system. Despite progress in treatment, these widespread types of malignant condition represent a serious health problem in the world. GI cancer is a multi-factorial and multi-stage involved disorder, its progression is influenced by environmental and genetic elements and the involvement of microbial population has also recently been recognized in many studies. Today, Next Generation Sequencing (NGS) approach has been used to elucidate the involvement of microorganisms in initiating and facilitating the process of GI cancer. In this chapter, we would like to clarify the role played by the gastrointestinal microflora in the genesis of GI cancers. This chapter will draw the state of the art in the study of the GI microbiota and how the dysbiosis could affect oncogenesis, tumor progression and response to cancer.