A rapid and simple method using ultra high performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) was developed for the determination of linamarin in cassava products and beans containing cyanogen compounds. Linamarin was extracted with acetonitrile–water (3 : 1) cleaned up using an amino solid-phase extraction cartridge, and then determined by UHPLC-MS/MS. The recoveries from cassava fortified at the levels of 10 μg/g and 100 μg/g were 96.1% and 95.3%, respectively, and their relative standard deviations were 2.6% and 1.4%, respectively. The recoveries from tapioca fortified at the levels of 1 μg/g, 10 μg/g and 100 μg/g were 81.1%, 91.9% and 97.1%, respectively, and their relative standard deviations were 3.3%, 5.4% and 2.1%, respectively. The contents of linamarin in 14 cassava, 9 tapioca and 4 butter bean samples were surveyed by this method, and linamarin was detected in the range of 0.1–245 μg/g in 11 cassava, 0.1–0.5 μg/g in 5 tapioca and 4,950–5,590 μg/g in 4 butter bean samples. The quantitation limit was 0.1 μg/g and the detection limit was 0.03 μg/g.