The Milk Composition Database (MCDB) is a freely available electronic database containing detailed information about small molecule metabolites found in cow milk. The MCDB contains a complete list of metabolite names, metabolite structures, level of verification (confirmed or probable), reference spectra (NMR, GC–MS and LC–MS) and citations for all (to the best of our knowledge) of the milk compounds that have ever been identified, quantified or reported either in this database or in the existing scientific literature. The database contains 2,355 metabolite entries including both water- and lipid-soluble metabolites as well as metabolites that would be regarded as either abundant (>1 uM) or relatively rare (<1 nM). Each metabolite entry contains more than 90 data fields and many of them are hyperlinked to other databases (KEGG, PubChem, ChEBI, PDB, MetaCyc, DrugBank, GenBank, and UniProt) and a variety of structure and pathway viewing applets. The MCDB itself is fully searchable and supports text, mass, spectral and structure searches. The information includes literature and experimentally derived chemical and molecular/biochemistry data.