The basophil activation test (BAT) is a flow-cytometry-based functional assay that assesses the degree of cell activation after exposure to a stimuli. Though no standardized technique currently exists, recent advances have improved the performance of this assay, including identification of new basophil-specific markers and comparisons of the expression of CD63 to CD203c during activation. The basophil activation test has also been validated for many IgE-mediated disease conditions, which have been extensively reviewed elsewhere. This review focuses on the most recent applications of this test to the diagnosis of allergy to drugs, foods, venoms, and pollens, and the evolving role of the BAT in monitoring immunotherapy.