Functional genomics provides new opportunities to address issues of fundamental interest in evolutionary biology and suggests many new research directions that are ripe for evolutionary investigation. New types of data, and the ability to study biological processes from a whole genome perspective, are likely to have a profound impact on evolutionary biology and ecology. To illustrate, we discuss how genomewide gene expression studies can be used to reformulate questions about trade-offs and pleiotropy. We then touch on some of the new research opportunities that the application of functional genomics affords to evolutionary biologists. We end with some brief notes about how evolutionary biology and comparative approaches will probably have an impact on functional genomics.