Mucositis induced by antineoplastic drugs is an important, dose-limiting and costly side effect of cancer therapy. The ulcerative lesions which result are frequent systemic portals of entry for microorganisms which inhabit the mouth and consequently are often sources of systemic infection in the myelosuppressed patient. A number of clinical observations and the inconsistency of responses to a broad range of treatment modalities suggests a physiological complexity to mucositis which has not previously been comprehensively considered. We now propose a hypothesis as to the mechanism by which mucositis develops and resolves, which is based on four phases: an initial inflammatory/vascular phase; an epithelial phase; an ulcerative/bacteriological phase; and a healing phase. The role of cytokines as initiators and ampliers of the process is discussed, as is the potential influence of genetic factors in establishing risk and modifying the course of stomatotoxicity.