The chicken has long been an important model organism for developmental biology, as well as a major source of protein with billions of birds used in meat and egg production each year. Chicken genomics has been transformed in recent years, with the characterisation of large EST collections and most recently with the assembly of the chicken genome sequence. Since the chicken shared a common ancestor with mammals 310 million years ago it fills a gap in our knowledge in the evolution and conservation of vertebrate genomes. As the first livestock genome to be fully sequenced it leads the way for others to follow. The genome sequence and the availability of 3 million genetic polymorphisms are expected to aid the identification of genes that control traits of importance in poultry. As the first bird genome to be sequenced it is a model for the remaining 9,600 species thought to exist today. Many of the features of avian biology and organisation of the chicken genome make it an ideal model organism for phylogenetics and embryology, along with applications in agriculture and medicine. In this report these advances are reviewed and the implications of the chicken genome in current and future applications are discussed.