The last decade has seen a significant acceleration in the introduction of molecular tools used in cancer diagnosis and treatment. Driving factors have been the movement of advanced technologies from the laboratory to the clinic and the shift to a more genetically individualised patient approach. With this has followed an increased ability to study the toxic side effects of cancer treatment, some of which are newly emerging, by utilising many of the same technologies. Mucositis research in particular has reached a golden period of investigation and understanding of the pathobiological mechanisms that contribute to the development of the condition. This paper has selected a few of the emerging technologies that are highly relevant to mucositis research to discuss in detail. These technologies include target therapies, toxicogenomics, nanomedicine, pharmacogenetics and pharmacogenomics, with a particular focus on microarray technology. These technologies are critical to discuss in the context of mucositis research not only because they are widely applicable to cutting edge research, but they also provide opportunities for further advances both in the laboratory and clinical setting. In addition, some of these technologies have the potential to be implemented immediately in the field of mucositis research.