Introduction: Allergen cross-contamination is a major food safety concern, as even trace amounts of allergens may cause severe adverse reactions in individuals with food allergies. Due to the wide variety of ingredients and the complexity of production processes, effective allergen management is essential in confectionery production. Purpose: The aim of this master's thesis was to investigate the risk of allergen cross-contamination with gluten and selected nuts in a small-scale confectionery facility and to evaluate the effectiveness of existing hygiene practices and the internal control system. Particular emphasis was placed on determining the presence of allergens in finished products, raw materials, and the production environment, as well as identifying their most likely sources. Methods: The study included a review of relevant scientific and professional literature, followed by an experimental investigation conducted in a selected confectionery facility. The presence of gluten and selected nuts was determined in finished products, raw materials, and environmental swab samples using real-time polymerase chain reaction (real-time PCR). Based on the initial analytical results, additional analyses of raw materials and environmental swab samples were performed to systematically identify and verify the most likely sources of the detected allergens. Results: The results showed that the unexpected presence of allergens in finished products was not caused by a single factor. In most cases, raw materials represented the primary source of allergen contamination, whereas the production process acted mainly as a secondary source of allergen transfer. By systematically linking the results obtained from finished products, raw materials, and environmental swabs, we enabled the identification of the most likely sources of allergen contamination in the majority of the investigated cases. Discussion and conclusion: Based on our findings, we concluded that effective allergen management requires a comprehensive approach that extends beyond appropriate hygiene practices and includes careful control of raw materials, effective cleaning of production equipment, and systematic allergen management throughout all stages of the production process. Based on the findings of this study, we developed a proposal for supplementing the existing internal control system with an additional chapter on allergen management, providing practical support for more effective prevention of allergen cross-contamination in the investigated confectionery facility.
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