Genome-wide association studies (GWAS) allow for a large number of samples to be assayed simultaneously, using a genome-wide tagging single nucleotide polymorphism (SNP) approach. The initial boon of success from disease studies such as macular degeneration and inflammatory bowel disease has been mitigated by lack of genome-wide significance for psychiatric disorders and related traits, despite evaluations of large populations. In addition to SNP genotypes, which are common variants typically attributing small or modest relative risk, copy number variations can be detected based on the same data set. Several rare recurrent copy number variations have been associated with psychiatric diseases in genome-wide analyses. Proper and responsible study design, followed by rigorous data quality assessment of genomic matching of cases and controls, is most likely to uncover regions of significant association that replicate in independent cohorts, thereby maximizing the chance of significant and confident association.