Functional genomics is transforming the way biological research is done in the 21st century. Functional genomics brings together high-throughput genetics with multiparallel analyses of gene transcripts, proteins, and metabolites to answer the ultimate question posed by all genome-sequencing projects: what is the biological function of each and every gene? Functional genomics is driving a shift in the research paradigm away from vertical analysis of single genes, proteins, or metabolites, towards horizontal analysis of full suites of genes, proteins, and metabolites. By identifying and measuring many, if not all of the molecular players that participate in a given biological process, functional genomics offers the prospect of obtaining a truly holistic picture of life. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline is likely to have in the future.