Different kinds of food products, such as cereal products, herbal teas, and honey, can be contaminated with various toxic substances originating from plants and fungi. Recently, plant toxins have drawn attention of researchers, as these are substances that appear in certain plants that are widespread and hence food contamination may occur. Some of the plant toxins that are known to have a negative impact on human body are tropane, ergot, and pyrrolizidine alkaloids. Currently, maximum permitted levels of these plant toxins do not exist (except tropane alkaloids in baby food) but can be expected soon as they are identified as a priority under the European Food Safety Authority. Considering the very complex and diverse composition of food, large number of plant toxins, and the effort to achieve the lowest limits of detection and quantification, only the methods with mass spectrometric (MS) detection provide the prerequisites to analyse plant toxins at ppb or ppt levels in food, either in combination with gas chromatography (GC) or high performance liquid chromatography (HPLC). Coupling of (UPLC) HPLC instruments with tandem mass- spectrometry (MS/MS) has become the method of choice for the analysis of plant toxins in recent years. The National Reference Laboratory for Mycotoxins, as part of Andrija Stampar Teaching Institute of Public Health, regularly monitors the development of mycotoxins in food and feed and provides scientific and technical assistance to the Ministry of Agriculture and the Ministry of Health in the development and implementation of a coordinated mycotoxin control programme, including plant toxins.