The Bovine Metabolome Database (BMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in bovines. It is intended to be used for understanding more about bovine biology and the micronutrients found in bovine tissues and biofluids as well as improving veterinary care for beef and dairy cattle. BMDB houses the comprehensive, quantitative metabolomic characterization of bovine biofluids and tissues, including serum, ruminal fluid, liver, longissimus thoracis (LT) muscle, semimembranosus (SM) muscle, and testis tissues. Using nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography-tandem mass spectrometry (LC-MS/MS), and inductively coupled plasma-mass spectrometry (ICP-MS), over 145 metabolites were experimentally identified and quantified in each of these biofluids and tissues. The full dataset combines these results with previous work on other bovine biofluids as well as previously published literature values for other bovine tissues and biofluids. Each metabolite entry (termed MetaboCard) contains not only the metabolite names and synonyms (common and IUPAC), but also their structures (multiple formats), basic descriptions, chemical ontology, physico-chemical properties, their reference spectra (NMR, GC-MS, and LC-MS), pathway information, and literature citations from the scientific literature. Many data fields are hyperlinked to other databases (HMDB, PubChem, MetaCyc, ChEBI, UniProt, and GenBank) and a variety of structure and pathway viewing applets. The BMDB database supports extensive text, sequence, chemical structure, and relational query searches.