The falling cost of DNA sequencing has made the technology af fordable to many research groups, enabling researchers to link genomic variants to observed phenotypes in a range of species. This review focusses on whole exome sequencing and its applications in humans and other species. The exome has traditionally been defined to consist of only the protein coding portion of the genome; a region where mutations are likely to affect protein structure and function. There are several commercial kits available for exome sequencing in a number of species and, owing to the highly conserved nature of exons, many of these can be applied to other closely related species. The data set produced from exome sequencing is many times smaller than that of whole genome sequencing, making it more easily manageable and the analysis less complex. Exome sequencing for disease gene discovery in humans is well established and has been used successfully to identify mutations that are causative of complex and rare diseases. Exome sequencing has also been used in a number of domesticated and companion species. The successful application of exome sequencing to crops has yielded results that may be used in selective breeding to improve production in these species, and there is potential for exome sequenc- ing to provide similar advances in livestock species that have not yet been realised.