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Isothiocyanates (ITCs) have a significant impact on food and natural product chemistry. Several dietary components and food chemicals contain the isothiocyanate moiety. In addition, many ITCs interact with macromolecules of biological relevance, making these compounds relevant for potential therapeutic applications and disease prevention. However, there is a lack of systematic analysis of ITCs in chemical and biological databases. Herein, we conducted a comprehensive analysis of ITCs present in public domain databases, including natural products, food chemicals, macromolecular targets of drugs, and the Protein Data Bank. A total of 154 ITCs were found, which can be classified into seven categories: acyclic, cyclic, polycyclic, aromatic, polyaromatic, indolic, and glycosylated. 24 ITCs were reported in 18 vegetable sources, mainly in cruciferous vegetables (Brassica oleraceaL.). Calculated properties of pharmaceutical relevance indicated that 11 % of the 154 ITCs would be suitable to be orally absorbed and 48 % permeate the blood‐brain‐barrier. It was also found that seven molecular targets have been co‐crystallized with ITCs and the most frequent is the macrophage migration inhibitory factor. It is expected that this work will contribute to the sub‐disciplines of natural products and food informatics.