Aim: Food-induced anaphylaxis is most common in the paediatric population and has an unpredictable course. The aim of this paper was to perform a demographic and clinical assessment of food-induced anaphylaxis in children using molecular diagnosis. Materials and methods: The study included 541 children aged 0–18 years who developed 893 sudden reactions to food. Levels of IgEs against 112 allergen molecules were measured in each child. We analysed demographic and clinical data in two age groups. The aetiology of anaphylaxis was determined at the level of source allergens and at the level of allergen molecules. We also determined the risk factors for severe clinical course of reactions. Results: A total of 631 food-induced anaphylactic reactions developed by 421 children were included in the analysis. The group of children aged 0–6 years was mostly composed of boys (p = 0.0023) and children with atopic dermatitis (p = 0.0001). Also, cutaneous and mucosal symptoms were more common (p < 0.0001), and milk casein, Bos d 8, was the most common cause of anaphylaxis in this group (p < 0.0001). In the group of 7–18-year-olds, anaphylaxis was more common in children with no asthma or atopic dermatitis (p = 0.0001); hazelnuts (p = 0.0005) and, in terms of allergen molecules, walnut 2S albumin, Jug r 1 (p = 0.0011), were a more common cause of reaction; as well as exercise-induced anaphylaxis (p < 0.0001) and cardiovascular symptoms (p = 0.0247) were more common. In the study population, more severe anaphylaxis was more common in children without asthma or atopic dermatitis (p = 0.0428) and in the case of anaphylaxis induced by cashew nut 2S albumin, Ana o 3 (p < 0.0001) and wheat allergen, Tri a 14 (p = 0.0143). Conclusions: Molecular diagnostics allows for a detailed assessment of the aetiology and the risk of severe food-induced anaphylaxis.