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Methods and compositions are provided for the diagnosis of allergen hypersensitivity in a patient. Rare, allergen-specific cells are enriched from a complex cell population, e.g. a patient blood sample. The percentage of blood cells that bind to a particular allergen is less than 0.01 %. The allergen-specific cell population is enriched by magnetic cell sorting. In normal blood, the allergen-binding cells are primarily B-cells expressing CD19 and CD21. In blood from allergic patients, an additional population of effector cells, e.g. basophilic granulocytes is labeled by the allergen.