Despite great interest in the role of the amygdala in animal and human behaviour, its very existence as a structurally and functionally unified brain component has been questioned, on the grounds that cell groups within it display divergent pharmacological and connectional characteristics. We argue that the question of whether particular brain nuclei constitute a valid structural and functional unit is inherently an evolutionary question, and we present a method for answering it. The method involves phylogenetic analysis of comparative data to determine whether or not separate regions of the putative brain structure show statistically correlated evolution. We find that, in three separate groups of mammals (primates and two groups of insectivores), evolutionary changes in the volumes of amygdala components are strongly correlated, even after controlling for volumetric change in a wide range of limbic and other brain structures. This allows us to reject the strong claim that the amygdala is neither a structural nor a functional unit, and demonstrates the importance of evolutionary analysis in resolving such issues in systems neuroscience.