The increasing public concern regarding the use of animals in biological research calls for the investigation of alternative approaches. Mathematical models are often seen as a possible alternative to animal experimentation but, to our knowledge, few models have been designed specifically for this purpose. Compared to other scientific disciplines, system-based approaches and modelling are relatively recent developments in biological sciences. One of the reasons for model development is the integration of current data, and several models have been developed to better understand the digestive and metabolic processes in farm animals. Although their construction required unavoidable animal experimentation, such models have proven very useful in further refining and orienting research questions, thereby avoiding redundant animal experimentation. Nutritional models can also be used in virtual experimentation to test the effect of different nutrients or feeding strategies on animal performance, nutrient utilization and excretion.