The Human Metabolome Database (HMDB) is a comprehensive and curated collection of human metabolite and metabolism data, currently the most extensive in the world. It contains records for over 2180 endogenous metabolites, with information gathered from various sources including books, journal articles, and electronic databases. The HMDB also includes experimental metabolite concentration data from mass spectrometry (MS) and Nuclear Magnetic Resonance (NMR) analyses of urine, blood, and cerebrospinal fluid samples. Each metabolite entry in the HMDB contains an average of 90 data fields, covering compound descriptions, names, synonyms, structural information, physico-chemical data, reference spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data, and links to images, references, and other databases. The HMDB provides extensive searching, relational querying, and data browsing tools to meet the needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists, and metabolomics researchers. It is available at www.hmdb.ca and is designed to address the broad needs of the metabolomics community. The HMDB is a multi-purpose database that combines molecular biology content from curated sequence databases with rich metabolic pathway and disease information, complemented by experimental data. The database is fully searchable and includes advanced features for higher-level database searching and selecting functions, such as chemical structure search, BLAST search, relational data extraction, and spectral matching tools. The HMDB is implemented as a web-friendly front-end to a sophisticated MySQL relational database and is maintained on a Linux server. The database is a work in progress, with constant additions and corrections, and is expected to serve as a useful model for future metabolomics databases.The Human Metabolome Database (HMDB) is a comprehensive and curated collection of human metabolite and metabolism data, currently the most extensive in the world. It contains records for over 2180 endogenous metabolites, with information gathered from various sources including books, journal articles, and electronic databases. The HMDB also includes experimental metabolite concentration data from mass spectrometry (MS) and Nuclear Magnetic Resonance (NMR) analyses of urine, blood, and cerebrospinal fluid samples. Each metabolite entry in the HMDB contains an average of 90 data fields, covering compound descriptions, names, synonyms, structural information, physico-chemical data, reference spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data, and links to images, references, and other databases. The HMDB provides extensive searching, relational querying, and data browsing tools to meet the needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists, and metabolomics researchers. It is available at www.hmdb.ca and is designed to address the broad needs of the metabolomics community. The HMDB is a multi-purpose database that combines molecular biology content from curated sequence databases with rich metabolic pathway and disease information, complemented by experimental data. The database is fully searchable and includes advanced features for higher-level database searching and selecting functions, such as chemical structure search, BLAST search, relational data extraction, and spectral matching tools. The HMDB is implemented as a web-friendly front-end to a sophisticated MySQL relational database and is maintained on a Linux server. The database is a work in progress, with constant additions and corrections, and is expected to serve as a useful model for future metabolomics databases.