Genome-wide association scans (GWAS) provide a mechanism to assess variation that segregates in a gene pool, rather than in a biparental population. Fashioned originally in human genetics, it has become popular in plant genetic research over the last decade [Waugh et al. (Curr Opin Plant Biol 12:218–222, 2009)]. GWAS is attractive because it potentially provides an opportunity to exploit existing and extensive phenotypic data collected during the plant registration process, thus making it directly relevant to current breeding material. It also holds the promise of increasing genetic resolution because GWAS populations typically contain more genetic breakpoints and more alleles than are found in conventional mapping populations. However, GWAS approaches also raise issues in genetic analysis. These are largely caused by the origins and history of the population, which introduce a tendency to reveal significant false-positive associations due to factors other than genetic linkage. Here, we summarise some of the progress and the problems that have been encountered in establishing effective GWAS in barley and the approaches that have been developed or applied to take account of them.