Until recently, definitions of avian genome structure and function were based solely on our knowledge of the chicken genome. The expansion of genomic studies to include nonmodel avian species allows us not only to refine those definitions but also to begin collecting the necessary resources to initiate a truly ecological genomics of birds. In this article we review new genomic technologies that will speed up the investigation of avian genome function. The streamlined nature of avian genomes implies that large-scale transcriptional analyses, studies of the role of regulatory elements and of developmental genes, and even the annotation of avian genomes will yield interesting surprises. We review promising methods used to investigate genome evolution in birds as well as the means by which to integrate functional genomics approaches and transcriptional profiling information into ecological and evolutionary studies.