Abstract Background The aim of our study was to determine the amount of mercury in Chamomile. In certain parts of Slovakia, such as Middle Spiš region in Eastern Slovakia, there has been reports of higher concentration of mercury in the soil. Heavy metals, including mercury, can enter human organism by ingestion. In case of using Chamomile infusions orally there is a risk of administration of mercury into the organism through digestive system. Methods We monitored mercury presence in Chamomile (Matricaria chamomilla) (n = 20) and the soil. We determined the mercury concentration by using the flameless atomic absorption spectrometer - Advanced Mercury Analyzer (AMA-254). Results Chamomile: The lowest concentration was in the roots (0.513 mg.kg-1). The second lowest was in the flower stem samples (1.105 mg.kg-1). The concentration of mercury was higher in the leaves (2.205 mg.kg-1). The highest was measured in the flower (2.541 mg.kg-1). Soil: The mercury content in soil in the entire territory of Slovakia is higher compared to the soil in the world. During our measurements, the concentration of mercury in the soil samples in the territory of Middle Spiš ranged from 100 to 500 mg.kg-1. Conclusions We have to take into account that the quality and contents of the soil are important for the crops, as it will entail their contents. With the knowledge of exceeded norms of mercury content in Slovak soils, it is crucial to monitor the mercury concentration in plants that are harvested there. Key messages • In the examined samples of Chamomile we found mercury, with its highest concentration in flowers and lowest in roots. • In the regions with significant mercury contamination it is crucial to monitor mercury content in harvested plants and to be cautious in regards of their consumption.