Chemotherapy is an effective anticancer treatment; however, it induces mucositis in a wide range of patients. Mucositis is the term used to describe the damage caused by radiation and chemotherapy to mucous membranes of the alimentary tract. This damage causes pain and ulceration, vomiting, bloating and diarrhoea, depending on the area of the alimentary tract affected. Although treatment is available for a small subset of patients suffering from mucositis, the majority rely on pain relief as their only treatment option. Much progress has been made in recent years into understanding the pathobiology underlying the development of mucositis. It is well established that chemotherapy causes prominent small intestinal and colonic damage as a result of up-regulation of stress response genes and pro-inflammatory cytokines. However, better understanding of the mediators of this damage is still required in order to target appropriate treatment strategies. Possible mediators of mucositis which have not been well researched are the matrix metalloproteinases (MMPs). MMPs have been shown to function in several of the pathways which are known to be up-regulated in mucositis and contribute to tissue injury and inflammation in many pathological conditions. This prompts the consideration of MMPs as possibly being key mediators in mucositis development.