Pyrrolizidine alkaloids are naturally occurring alkaloids found in different species of herbal medicines such as Arnebia euchroma, Eupatorium fortunei, Eupatorium lindleyanum, Senecio scandens, Symphytum officinale, and Tussilago farfara. In the early of 1900s, pyrrolizidine alkaloids were reported to be potentially hepatotoxic, carcinogenic, and genotoxic in human and animals by many researchers. Thus, the governments of various countries begin to pay much attention to the safety issues of pyrrolizidine alkaloids in use of these plants as foods or drugs. The acceptance criteria of pyrrolizidine alkaloids in Senecio scandens has been established in the Pharmacopoeia of the People's Republic of China. The content of pyrrolizidine alkaloid adonifoline (C18H23NO7) should be not more than 0.004% by liquid chromatography-mass spectrometric analysis (LC-MS). Arnebia euchroma is main composition of Tzu-Yun Ointment, a traditional Chinese medicine used for the treatment of skin disorders. Literatures reported Arnebia euchroma contained pyrrolizidine alkaloids 7-angeloylretronecine and 9-angeloylretronecine at the total concentrations of about 10 ppm. For the advanced identification of pyrrolizidine alkaloids in Arnebia euchroma and Tzu-Yun Ointment, Herbiotek applied Liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the presence of 7-angeloylretronecine (C13H19NO3) and 9-angeloylretronecine (C13H19NO3). The results showed these pyrrolizidine alkaloids were actually present in Arnebia euchroma as the literature reports. However, they were not detected in Tzu-Yun Ointment under the same analytical condition. The rationale was proposed due to their poor solubilities in oily base formulation of Tzu-Yun Ointment. The concentrations of pyrrolizidine alkaloids in Tzu-Yun Ointment were considered less than 1 ppb (μg/kg) based on the detection capacity of LC-MS/MS analysis.