Cyanogenic glycosides are a large group of secondary metabolites that are widely distributed in the plant kingdom, including many plants that are commonly consumed by humans. The diverse chemical nature of cyanogenic glycosides means that extraction and analysis of individual compounds can be difficult. In addition, degradation can be rapid under appropriate conditions. Amygdalin is one of the cyanogenic glycosides found, for example, in apples, apricots and almonds. We have developed and applied a high performance liquid chromatographic procedure for amygdalin quantification to investigate extraction efficiency and to determine levels in a range of commercially-available foods for the first time. Our results show that seed from Rosaceae species contained relatively high amounts (range 0.1–17.5mgg−1) of amygdalin compared to seed from non-Rosaceae species (range 0.01–0.2mgg−1). The amygdalin content of processed food products was very low.