Allergies are hypersensitive reactions that affect over 25% of the world population. Extensive studies have been directed to define patho-immunological mechanisms of allergy and the molecular characteristics of allergens. The emerging B cell and T cell epitope database has greatly facilitated the development of epitope-based immunotherapy that aims at modulating patients’ immune responses towards a specific allergen. Modifications on the B cell epitopes reduce the affinity of allergens towards IgE while inducing immuno-tolerance as in traditional therapies utilizing native allergens. T cell epitope-based immunotherapy is considered as a safe form of therapy since the small peptide fragments cannot form cross-links with IgE. In this review, current strategies in mapping B cell and T cell epitopes are discussed. Furthermore, current progress in the translation of epitope into potential immunotherapies is illustrated with specific examples on airway and food allergies.