Celiac disease (CD), a chronic enteropathy of the small intestine caused by ingestion of gluten, is one of the most prevalent food hypersensitivities worldwide. The essential treatment is a strict lifelong gluten-free diet based on the avoidance of gluten-containing products from wheat, rye, barley and, in rare cases, oats. Products made from naturally gluten-free raw materials often have inferior nutritional, textural and sensory properties compared to the corresponding gluten-containing products. Therefore, the incorporation of wheat, rye and barley flours after efficient removal of the harmful component gluten into gluten-free products would be beneficial. Gluten modification resulting in decreased CD-immunoreactivity may be achieved via the formation of crosslinks using microbial transglutaminase. To effectively eliminate CD-immunoreactivity, plant, fungal, bacterial, animal or engineered peptidases are capable of degrading gluten proteins and peptides into harmless fragments. The application of peptidases from germinated cereal grains, fungal peptidases and/or lactic acid bacteria during food processing yielded high-quality sourdough wheat breads, pasta, wheat starch and bran, rye products and beer, all with gluten contents below the Codex Alimentarius threshold of 20mg/kg for gluten-free products. As with all gluten-free products, the legislative compliance of such treated materials needs to be monitored closely. Provided that all safety requirements are met, gluten-containing raw materials treated in an adequate way to remove CD-active gluten fragments may be used together with naturally gluten-free ingredients to create an extended choice of high-quality gluten-free products.