Berberine is an isoquinoline alkoaloid found in a number of Chinese herbs including Goldenthread (coptis chinensis) and the bark of phellodendron amurense. Among western herbs, berberine appears in varying concentrations in western barberry (Berberis vulgaris), Oregon grape (Berberis aquifolium), tree turmeric (Berberis aristata) and goldenseal (Hydrastis Canadensis). The Berberine alkaloid appears in the roots, rhizomes and bark.

Berberine hydrochloride or sulfate is considered most effective as an herbal treatment. Berberine appers to be most effective as an antiseptic in chloride form. 

Berberine chloride from plant roots and stems also is the primary ingredient in Natural Yellow 18, a dye from natural sources.

Berberine should not be used during pregnancy as it may cause uterine contractions and miscarriage. It has also been linked to neonatal jaundice. Berberine in very large doses for more than 4-6 weeks may cause liver overload. However doses of 200-1200mg have been found to be safe for most patients.