Genome organisation can be considered at a number of levels from the karyotype to gene order, copy number variation and the organisation of chromosome territories and loci within the interphase nucleus (nuclear organisation). Detailed studies of these areas in birds however are limited. As the only bird with a published genome sequence, and for its importance in areas such as agriculture, developmental biology and evolutionary studies, the chicken (Gallus gallus) is the most studied bird. Comparative genomics provides a powerful method for transferring information from the chicken to other, less well studied species. An obvious target for comparative genomic studies in birds is the Pekin duck (Anas platyrhynchos), for its agricultural significance, resistance to avian influenza, and evolutionary relationship to chicken. This thesis reports comparative genomic studies in duck and other birds. A method for easy assignment of physical markers to chromosomes was established through the measurement of relative sizes of chicken, duck and turkey chromosomes. Physical mapping in the duck revealed previously undescribed chromosomal rearrangements, provides further evidence for conserved synteny among avian microchromosomes and yields an improved definition of the duck karyotype. A detailed study of nuclear organisation was carried out in chicken fibroblasts; this baseline was used to investigate patterns of nuclear organisation in turkey (Meleagris gallopavo) and duck fibroblasts, and in activated chicken and duck macrophages. Finally, microarray based comparative genomic hybridisation studies of copy number variation (CNV) were conducted in 10 bird species to complement the lower resolution cytogenetic mapping. These suggest that CNVs are less frequent in birds than in mammals, yet more commonly associated with genes. This work improves our understanding of avian genomics and evolution.