Canada and Australia both aspire to have a vibrant biomedical sector, but their performance is very different. The paper uses innovation systems theory to search for reasons for these differences. It develops, within a knowledge framework, a set of indicators to measure the dynamic performance of the two sectors. The results suggest that the dynamics of the Canadian biomedical innovation system have been positively reinforcing, while the Australian under performance has been the product of its failure to effectively use the knowledge generated and diffused within the innovation system. The results support the use of the innovation systems approach