Isoquinoline alkaloids (papaverine, noscapine, berberine, emetine, and quinine) were determined in medicinal plants and herbs used in Traditional Chinese Medicine and Ayurveda by liquid chromatography with tandem mass spectrometry detection (LC-MS/MS). The analyzed alkaloids were separated at gradient conditions using methanol and 2% acetic acid within 12min. The validated method was successfully applied for 17 herbal samples: Ashwagandha, Astragalus membranaceus, Emblica officinalis, Mucuna pruriens, Pueraria lobata, Ocimum sanctum, Rehmannia glutinosa, Schisandra sinensis, Terminalia arjuna, Terminalia chebula, and dietary supplements. The highest concentration of studied alkaloids was observed for berberine in Puearia lobata (6.68 +/- 0.62mg 100g(-1) d.m.), while the lowest value was obtained for noscapine in a dietary supplement containing Terminalia arjuna (0.09 +/- 0.01mg 100g(-1) d.m.). Principal component analysis, cluster analysis, and one-way ANOVA tests were also performed. The results indicate the need to control plant materials and dietary supplements in terms of the content of alkaloids and toxic components.