Geneticists have made tremendous progress in understanding the genetic basis of phenotypes, and genomics promises to bring further insights at a rapid pace. The progress in functional genomics has been driven primarily by the development of new techniques that are used in a few dedicated research centres. Focusing on selected advances in genomic technologies, we assess the results that have been obtained so far, highlight the challenges faced by these new tools and suggest ways in which they can be overcome. We argue that progress in functional genomics will depend on developing high-throughput technologies that can easily be moved away from dedicated centres and into individual laboratories.