This chapter is an extensive review of allergen-based diagnostic methodologies including old techniques such as skin prick test, radio-allergo sorbent test, enzymelinked immunosorbent assay, and fluorescent-enzyme immunosorbent assay. Novel technologies include functional tests by flow cytometry and molecular allergy based on multiplex immunoassays. We also review the importance of biochemical characteristics of allergens, sensitivity and specificity, cross-reaction between allergens, utility, reproducibility, interpretation, and methodologies for discovery of epitopes for diagnostic or therapeutic use.