Genome-wide association studies have had a huge impact on the field of human genetics. They have identified new genetic risk factors for many common human diseases and have forced the genetics community to think on a genome-wide scale. On the horizon is whole-genome sequencing. Within the next few years we will see the arrival of cheap sequencing technology that will replace one million SNPs with the entire genomic sequence of three billion nucleotides. Challenges associated with data storage and manipulation, quality control and data analysis will be manifold more complex, thus challenging computer science and bioinformatics infrastructure and expertise. Merging sequencing data with that from other high-throughput technology for measuring the transcriptome, the proteome, the environment and phenotypes such as the massive amounts of data that come from neuroimaging will only serve to complicate our goal to understand the genotype-phenotype relationship for the purpose of improving healthcare. Integrating these many levels of complex biomedical data along with their coupling with experimental systems is the future of human genetics.