Current advances in our understanding of molecular evolution of immunity in jawed vertebrates are summarised. Moreover, the immunome concept is introduced in the paper. The immunome serves as a framework for characterizing genes involved in immune defence from a comparative perspective. The second focus is on different selection modes that are observed across groups of immune genes, and hypotheses are proposed to explain these differences. An overview of the approaches used so far to study the evolutionary heterogeneity of immune genes are provided on macro and microevolutionary scales. Finally, some of the available evidence as to how specific pathogens affect the evolution of different groups of immune genes is discussed.