Allergy is a prevalent health problem in developed countries. With advances in genomic and proteomic technologies, there is a rapid increase in allergy-related data, including allergen sequences, allergic cross-reactivity, molecular structures, clinical measurements, and atmospheric concentrations. The more and more complex allergy data is fueling the need for advanced ways in information management and analysis. Computational methods and resources are increasingly the driving force in allergy research. For example, allergen-specific databases are important data sources for allergen characterization. T-cell and B-cell epitope prediction tools focus on identifying immunogenic regions on allergenic proteins. Allergenicity and cross-reactivity prediction tools are increasingly being applied to assess the potential allergenicity of proteins. This review provides an introduction to the growing literature in this area, with particular emphasis on recent developments in bioinformatics relevant to the study of allergens.