Berberine, a fluorescent, aromatic, heterocyclic alkaloid, produced in a diversity of plants, was found to have curative properties in Chinese herbal medicine. Berberine is used as a treatment for gastric and inflammatory diseases and as an antimicrobial agent. More recently the potential of this alkaloid in diverse new medical application like cardiology, neurology and oncology is being investigated. As a result of its fluorescent properties, it has also been used in chemistry to study protein conformation and protein/protein interactions and to quantitate non-fluorescent compounds. All these applications will be summarized and discussed in this review.