Genome-wide association studies (GWAS) have revolutionized human genetics. They have led to the identification of thousands of loci that affect both normal variation and susceptibility to disease, and have clarified our understanding of the genetic architecture of complex traits. In just five years, the methodology has moved from extraordinary to commonplace, and with the advent of affordable genome-scale data collection, GWAS and other genomic technologies are being adopted by model organism researchers. As GWAS applications have evolved so too have the community standards that pertain to them. Here we clarify the editorial policy of PLoS Genetics with regard to these guidelines.