Chickens have undergone intensive selection to produce highly productive strains with excellent growth rates and feed conversion ratios. There does not appear to be any reduction in the rate of strain improvement. The recently completed chicken genome sequencing project and adjunct projects cataloging single nucleotide polymorphisms demonstrate that there is still a high level of genetic variation present in modern breeds. The information provided by genome and transcriptome studies furnishes the chicken biologist with powerful tools for the functional analysis of gene networks. Gene microarrays have been constructed and used to investigate gene expression patterns associated with certain production traits and changes in expression induced by pathogen challenge. Such studies have the potential to identify important genes involved in biological processes influencing animal productivity and health. Fundamental regulatory mechanisms controlled by non-coding RNAs, such as microRNAs, can now be studied following the identification of many potential genes by homology with previously identified genes from other organisms. We demonstrate here that microarrays and northern blotting can be used to detect expression of microRNAs in chicken tissue. Other tools are being used for functional genomic analysis including the production of transgenic birds, still a difficult process, and the use of gene silencing. Gene silencing via RNA interference is having a large impact in many areas of functional genomics and we and others have shown that the mechanisms needed for its action are functional in chickens. The chicken genome sequence has revealed a large number of immune related genes that had not previously been identified in chickens. Functional analysis of these genes is likely to lead to applications aimed at improving chicken health and productivity.