Pathway analysis helps to elucidate the complex structures of cellular networks that are needed to understand pathogenetic processes on a systems level. It may also help to identify pathways that are significantly affected in disease. Thus, it is an essential step in identifying and prioritizing novel drug targets. In this article, we discuss group tests for identifying significantly altered pathways in genome-wide data, pathway representations for mathematical modelling and pathway analysis methods to find nodes in pathways that are of crucial importance. This is followed by some examples of the successful modelling of signal transduction pathways.