Different technological processes are required in food industry to process plant- and animal-derived raw materials in order to make the long-term storage of foodstuffs possible and their consumption safe. During the production of foodstuffs, various technological methods, both thermal (pasteurization, ultrasounds, microwaves, roasting, and autoclaving) and non-thermal (enzymatic modifications, sprouting, ultra-filtration, gamma-radiation, high pressure, homogenization, and grinding) are used to process raw materials. Apart from the changes in physical properties and the microbial stability gained, in most cases, the allergenic potential of ready-made product is changed, too. Higher quantities of processed foods are introduced into the market and this fact is one of the main reasons why the number of persons allergic to food increases. The novel processing technologies can either decrease the allergenicity of final products as compared to that of raw materials or they can be a direct cause of new, up to now unknown allergens, constituting an identification problem for immune systems.