The major challenge in allergy diagnosis is development of accessible and reliable diagnostics that can predict the clinical outcome following exposure to culprit allergen(s) or cross-reactive molecules and identification of safer alternatives than the current state-of-the-art methods. There is accumulating evidence that flow-based analyses for the quantification of activated basophils and mast cells subsequent to in vitro challenge (the basophil and mast cell activation test [BAT/MAT] or basophil activation test [BAT] and mast cell activation test [MAT]) could meet the diagnostic requirements for IgE-dependent allergies, drug hypersensitivities, and subsets of autoimmune urticaria. Furthermore, the BAT and MAT have found application in research and other nondiagnostic fields. However, appropriate use of the BAT and MAT requires understanding of the diversity of the source materials used and degranulation metrics to ensure correct test performance and interpretation of results. In this review, we provide the main applications and limitations of the BAT and MAT, as performed thus far.