Cancer patients receiving chemotherapy often develop mucositis as a direct result of their treatment. Recently, the intestinal microbiota has attracted significant attention in the investigation of the pathobiology of mucositis, with a number of studies investigating the effects of chemotherapeutic agents on the microbiota. With significant effects on the intestinal microbiota occurring following the administration of chemotherapy, there is now interest surrounding the downstream pathological effects that may be associated with the altered intestinal ecology. This review seeks to identify links between signalling pathways previously demonstrated to have a role in the development of mucositis, and the altered intestinal microbiota.