Despite potential health benefits of cookies with seeds, e.g., antioxidant and anticholesterolemic activity, their baking may lead to processing contaminants. This study investigated the acrylamide formation in cookies containing chia and flaxseeds (13 samples) in various formats and amounts by LC–MS/MS using stable isotope dilution analysis. Furthermore, the impact of different factors was studied. Cookies with chia seeds (Salvia hispanica L.) exhibit increased acrylamide contents from whole (112–286 μg/kg) to milled seeds (252–649 μg/kg). Acrylamide contents of cookies with whole or milled flaxseeds (Linum usitatissimum) (204–516 μg/kg) were comparable to those with chia seeds, while cookies with flaxseed flour had the highest exposure (790 μg/kg). Adding baking agents to cookies with chia seeds increased acrylamide by 20 %, while organic acids significantly lowered it (up to 78 %). The sugar source affected acrylamide in cookies with chia seeds, with brown sugar resulting in the highest content (213 μg/kg).
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