Oral mucositis can be a significant problem for cancer patients and is frequently seen in the patient population receiving high-dose head and neck radiation therapy (85%-100%), stem cell transplantation (75%-100%), and myelosuppressive chemotherapy for solid tumors (5%-40%). Current guidelines published through the joint efforts of the Multinational Association of Supportive Care in Cancer and the International Society for Oral Oncology recommend strategies for the prevention and treatment of mucositis in the setting of radiation therapy, chemotherapy, and combined chemoradiation therapy. An improved understanding of its pathologic basis has led to the development of targeted agents to combat mucositis. One of these drugs, palifermin, is a keratinocyte growth factor agent approved for patients with hematologic malignancies receiving myelotoxic therapy requiring hematopoietic stem cell support. Another agent is AES-14, an uptake-enhanced L-glutamine suspension that has shown efficacy in phase III trials in reducing the risk of developing oral mucositis in breast cancer patients receiving chemotherapy. As the understanding of the pathobiology of mucositis improves, clinicians should be able to customize future therapies based on each patients risk for developing the condition.