An enormous number of high-quality Web-based resources are now available to facilitate research into genome variation. Although identification of the most appropriate and informative resources can be challenging, a number of key sites provide links to more specialized resources that may be useful to follow up. Given ongoing research, focussing on the sequencing of many different genomes, we can expect sequence databases and their associated polymorphism-based resources to greatly increase in depth and complexity in a relatively short period of time. However, databases and tools developed to date, and described here, provide a sound basis for accommodating this next generation of genomic data. As well as sequence-oriented resources this review presents databases providing genotypic and common disease phenotype data, copy number variation, genetic maps, cytogenetic data, and gives an overview of key software tools, with the emphasis on analysis of the genetic basis of common disease.