The Human Metabolome Database (HMDB) is a comprehensive, freely available web resource containing detailed information about the human metabolome. HMDB 4.0, the latest version, represents the most significant upgrade to the database in its history. It includes a threefold increase in fully annotated metabolites, a fourfold increase in experimental spectra, and a 60-fold increase in illustrated metabolic pathways. The database has also improved its chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. HMDB 4.0 contains 114,100 metabolites, with 279,972 predicted MS/MS spectra and 38,277 predicted GC–MS spectra. It also includes 25,570 illustrated metabolic pathways and 5,498 metabolite-disease associations. New data content includes pharmacometabolomics data, metabolite-SNP interactions, and a new functional ontology. The HMDB interface has also been enhanced with improved pathway viewing, spectral viewing, and searching tools. HMDB 4.0 is now more compatible with multi-omic studies and provides better data exchange standards. The database is intended to facilitate research in human nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.The Human Metabolome Database (HMDB) is a comprehensive, freely available web resource containing detailed information about the human metabolome. HMDB 4.0, the latest version, represents the most significant upgrade to the database in its history. It includes a threefold increase in fully annotated metabolites, a fourfold increase in experimental spectra, and a 60-fold increase in illustrated metabolic pathways. The database has also improved its chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. HMDB 4.0 contains 114,100 metabolites, with 279,972 predicted MS/MS spectra and 38,277 predicted GC–MS spectra. It also includes 25,570 illustrated metabolic pathways and 5,498 metabolite-disease associations. New data content includes pharmacometabolomics data, metabolite-SNP interactions, and a new functional ontology. The HMDB interface has also been enhanced with improved pathway viewing, spectral viewing, and searching tools. HMDB 4.0 is now more compatible with multi-omic studies and provides better data exchange standards. The database is intended to facilitate research in human nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.