The Human Gene Mutation Database (HGMD) constitutes a comprehensive core collection of data on germ-line mutations in nuclear genes underlying or associated with human inherited disease ( http://www.hgmd.org). Data catalogued include single base-pair substitutions in coding, regulatory and splicing-relevant regions, microdeletions and microinsertions, indels, triplet repeat expansions, as well as gross gene deletions, insertions, duplications and complex rearrangements. Each mutation is entered into HGMD only once in order to avoid confusion between recurrent and identical-by-descent lesions. By December 2009, the database contained in excess of 96,600 different lesions detected in 3,611 different nuclear genes, with new entries currently accumulating at a rate in excess of 9,000 per annum. Since its inception, HGMD has been expanded to include cDNA reference sequences for more than 95% of the listed genes, splice junction data, disease-associated and functional polymorphisms, and links to data present in publicly available online locus-specific mutation databases. Although HGMD currently has a licensing agreement with BIOBASE GmbH (Wolfenbüttel, Germany) to distribute the very latest mutation data to subscribers, the bulk of HGMD mutation data will continue to be made freely available via the Internet. HGMD data have been used to perform a number of meta-analyses involving a variety of different types of mutational lesion, e.g., single base-pair substitutions within both coding and regulatory regions, indels, gross deletions, gross insertions, microdeletions and microinsertions. The major outcome of these studies has been the recognition that human gene mutation is a highly sequence-specific process, a notion that has important implications for the nature, prevalence and diagnosis of human genetic disease.