The prevalence of allergic diseases in Poland and in the world continues to rise in recent years. The most commonly used methods for diagnosing IgE – dependent allergies are skin prick testing (SPT) and assessment of specific IgE (sIgE) directed against specific allergens. However, both methods have some disadvantages and the obtained results may be inconsistent. In particular, routine diagnostic tests are not always effective for some drugs and foods. Consequently, additional laboratory tools should be used. Basophil activation test (BAT) based on flow cytometry is a promising diagnostic method. The present paper demonstrates the usefulness and effectiveness of BAT protocols in allergy diagnosis in scientific research. In comparison to routinely used diagnostic methods, BAT is an expensive and complicated laboratory tool. However, it offers the possibility to efficiently and effectively recognize allergies. Introducing BAT into routine diagnostics in allergology is problematic because this method has not yet been standardized and validated. Therefore, there is a justified need to continue research in this field. If standardized and validated, BAT may offer a reasonable improvement in allergy diagnostics in the future.