The Cannabis Compound Database is a freely available electronic database containing detailed information about small molecules found in Cannabis sativa, Cannabis indica and Cannabis hybrids – both within the plant itself and in Cannabis smoke condensate. This database is intended to provide detailed, well-researched, authoritative information about a wide variety of known Cannabis chemicals, their abundance within various Cannabis cultivars, their physiological/medicinal effects, and their known (human) protein targets. The Cannabis Compound Database is designed to contain and link cannabis chemical data with human physiological and molecular biology/biochemistry data. The database contains 6,172 chemical constituent entries and 2,336 chemical concentrations for 115 Cannabis cultivars. Extensive compound descriptions along with more than 514 references are provided. Additionally, 5,207 human protein sequences (protein targets) are linked to these chemical entries. The Cannabis Compound Database also contains 50,817 MS/MS spectra (predicted and experimental), 1,529 NMR spectra (experimental) and 5,929 GC-MS spectra (predicted and experimental) to facilitate compound identification and characterization of Cannabis cultivars and Cannabis products. Many data fields in the database are hyperlinked to other databases (FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank). The Cannabis Compound Database supports extensive text, sequence, spectral, chemical structure and relational query searches.