Allergy to plant-derived foods is a highly complex disorder with clinical manifestations ranging from mild oral, gastrointestinal, and cutaneous symptoms to life-threatening systemic conditions. This heterogeneity in clinical manifestations has been attributed to different properties of allergenic molecules. Based on this fact, symptom elicitors were grouped into class I and pollinosis-associated class II food allergens, but clear distinction is rather ambiguous. Moreover, mechanisms underlying food sensitization are not fully understood yet, and food allergy management most often relies on patient's compliance to avoid suspected foods. Therefore, recent efforts aim at the investigation of plant food allergies at the molecular level. This review provides an overview on currently available techniques for allergen characterization and discusses their application for investigation of plant food allergens. Data obtained by an array of physicochemical analyses, such as allergen structure, integrity, aggregation, and stability, need to be linked to results from immunological methods at the level of IgE and T-cell reactivity. Such knowledge allows the development of computational algorithms to predict allergenicity of novel foods being introduced by biotechnological industry. Furthermore, molecular characterization is an indispensable tool for molecule-based diagnosis and future development of safer patient-tailored specific immunotherapy in plant food allergy.