Food allergy represents an important food safety issue and the only effective treatment is the complete removal of the allergen from diet. However, food formulation are becoming more complex which means that foods may be unintentionally contaminated via allergen-containing ingredients or cross contamination affecting consumers, food companies and competent authorities. To tackle food allergen issue, food industry and control agencies rely on analytical methods to quantify the amount of a particular allergic commodity in a food. Nowadays mostly receptor based methods and in particular commercial kits are used in routine analysis. However, during processing chemical changes in allergens/proteins occur which affect the analytical outcome with issues related to extractability and matrix effects being the biggest challenge. Therefore, food industry needs to make extra efforts to provide accurate labeling and to reduce the contamination with allergens.