At present, animal experimentation remains central to our understanding of human disease-related processes and of the biological effects of many substances. Traditional experiments have relied heavily on invasive techniques to monitor changes in blood biochemistry, tissue structure or function, or to phenotype or genotype genetically modified animals. In some cases, a proportion or all of the animals used during the course of a study may be sacrificed for histopathological assessment. In most cases, this is to track the progression or regression of a disease over time, or to determine the levels of toxicity evident in specific organs or tissues. However, many of these techniques fail to provide details of how a disease develops or how a substance elicits its effects. In recent years there has been a gradual increase in the application of imaging techniques that were originally developed and used in fundamental research or in medicine. These non-invasive techniques allow diseases, and responses to exogenous substances, to be monitored in a temporal and spatial manner, therefore allowing a greater amount of information to be derived from smaller numbers of animals, which in turn, increases the statistical validity of the data by reducing the level of experimental variation. Non-invasive imaging also allows more informative and humane endpoints to be used and, perhaps most importantly, allows functional details to be studied in the context of a living animal. Some of the recent developments within the field of non-invasive imaging and their significance with respect to animal welfare and the understanding of human physiology are discussed.