Crop plants are important foods that provide necessary energy in human diets but can cause allergic reactions resulting in serious health problems. Therefore, it is necessary to identify allergens in crop plants to determine causative allergenic foods in patients and facilitate allergen diagnosis. Recent advances in proteomic approaches have significantly contributed to the detection and identification of food allergens. Proteomic techniques can also reveal the qualitative and quantitative variability of allergens among crops and changes in the proteome constitution of crops following genetic modification. Moreover, allergen identification and characterization are important for the diagnosis of food allergies and risk assessment of genetically modified crops as food sources. In the present review, we discuss how proteomics can be applied to detect and identify allergens in plant-derived foods.