Runs of homozygosity (ROH) are long, contiguously homozygous portions of the genome. Regions have emerged where a very large or small proportion of the population share a ROH; these regions are called ROH islands or deserts. By understanding the diversity in a population and where that diversity, or lack thereof, is in the genome, breeders will be able to preserve diversity, target production-related alleles, and understand how individuals and populations are related. Studies on ROH have been done in humans, cattle, pigs, and chickens. ROH islands, have, until now, only been identified in humans and cattle. In this study we try to answer the following questions: Do we find ROH islands and deserts that occur across a wide spectrum of chicken breeds with different breed history and origin and if so, where? How gene dense are islands and deserts and how do they compare with the rest of the genome? What genes do we find in islands and deserts? What level of haplotype diversity is found in islands and how are the various haplotypes related? Eighty-two diverse populations of chickens from Europe and Asia were analysed including fancy breeds, commercial lines of layers and broilers, and two populations of Red Jungle Fowl. Populations were genotyped using the Affymetrix Axion ® Genome-Wide Chicken Genotyping Array 600k chip, 1677 individuals were analyzed in this study. We found that ROH islands and deserts occur frequently in macro- and microchromosomes. Islands are found across all breed groups and are likely ancestral in origin. A wide range of genes with varying functions and pathways are found in islands. The haplotypes discovered in islands are mainly shared across breed groups indicating very recent separation of breeds. The patterns of islands and deserts found in chickens is clearly different from those found in other species. This necessitates a unique approach to the search for, and interpretation of, these fascinating regions.