Genome-wide association studies (GWAS) aim to identify genetic variants across the whole genome associated with the phenotype of interest. This technique has been largely used in the bone field to elucidate the genetic architecture of complex traits, like bone mineral density or fracture risk, and to date, more than 600 loci have been identified. To ensure that the associations are reliable, a careful design is required, depending upon the phenotype and the sample size, as well as the implementation of adequate quality control measures at both variant and sample levels. There is several software freely available to perform these studies, and different approaches can help increase the number of analyzed genetic variants, like imputation, or the sample size (meta-analysis). Further post-GWAS analysis can be applied to investigate the possible biological function and potential therapeutic relevance of the identified loci.