A combination of both environmental and genetic factors contributes to the vast majority of human cancers and in particular cancers of the gastrointestinal tract, including the stomach, colon and rectum. The mechanisms associated with cancer causation or prevention are largely unknown and the subject of much research. Many of these mechanisms implicate the metabolic activities of the bacterial flora normally resident in the gastrointestinal tract. This paper examines both the detrimental and beneficial consequences of bacterial activity of the gastrointestinal tract, focusing in particular on the stomach and large intestine.