Food allergy represents an important food safety issue because of the potential lethal effects; the only effective treatment is the complete removal of the allergen involved from the diet. However, due to the growing complexity of food formulations and food processing, foods may be unintentionally contaminated via allergen-containing ingredients or cross-contamination. This affects not only consumers' well-being but also food producers and competent authorities involved in inspecting and auditing food companies. To address these issues, the food industry and control agencies rely on available analytical methods to quantify the amount of a particular allergic commodity in a food and thus to decide upon its safety. However, no "gold standard methods" exist for the quantitative detection of food allergens. Nowadays mostly receptor-based methods and in particular commercial kits are used in routine analysis. However, upon evaluation of their performances, commercial assays proved often to be unreliable in processed foods, attributed to the chemical changes in proteins that affect the molecular recognition with the receptor used. Unfortunately, the analytical outcome of other methods, among which are chromatographic combined with mass spectrometric techniques as well as DNA-based methods, seem to be affected in a comparable way by food processing. Several strategies can be employed to improve the quantitative analysis of allergens in foods. Nevertheless, issues related to extractability and matrix effects remain a permanent challenge. In view of the presented results, it is clear that the food industry needs to continue to make extra efforts to provide accurate labeling and to reduce the contamination with allergens to an acceptable level through the use of allergen risk management on a company level, which needs to be supported inevitably by a tailor-validated extraction and detection method.