For some years now the basophil activation test (BAT) using flow cytometry has emerged as a powerful tool and sensitive marker that can be used to detect clinically relevant allergies, provide information on the severity of an allergic reaction, and monitor therapies. Compared to other in vitro diagnostic tests, BAT seems to have a better informative value in terms of clinical relevance. In general, the BAT can be used for the diagnosis of the most common forms of IgE-mediated allergy such as hymenoptera venom allergy, inhalant allergy, food allergy, and drug allergy. Various basophil markers and parameters have been established which, depending on the trigger of the respective allergy, can provide information on the clinical relevance of sensitization, on the development of natural tolerance, on trigger thresholds, and on the severity of the allergic reaction. The BAT also serves as a suitable follow-up instrument for various therapeutic approaches such as specific immunotherapy, desensitization protocols, or use of anti-IgE-antibodies for the various diseases. Quality controls for routine use, standardization, and automatization are expected to expand the range of applications for the above-mentioned indications.