The origin of metal elements in tonsillar tissues of children patients was investigated in order to establish the link between environmental pollution and tonsilitis diagnosis. The children lived either in a polluted, industrial region (Moravian-Silesian Region, North-East Czechia) or a clean, predominantly agricultural region (South Bohemian Region, South-East Czechia). Simultaneously, the distance of the address of the patients to the closest main road was assessed. The elemental content of the present particulate matter in the tonsil samples, coming from indicated tonsillectomies, was analysed using scanning electron microscopy equipped with an X-ray microprobe. No significant association of the elemental composition and the region was found using both bivariate and multivariate methods; however, an association with the distance to the closest main road was found. The study presents a novel assessment of the tonsillar tissues and supports the link between environmental factors (traffic-related particulate pollution) and the onset of chronic, idiopathic diseases in children, which has been debated recently.