Background Basophil activation tests can provide valuable information on allergic sensitivity to a range of different allergens. The most widely employed methods involve flow cytometric detection of increased expression of membrane-bound CD63 or CD203c following addition of allergen to basophils in vitro. The identification of basogranulin, a unique basic protein stored in basophil granules, has opened the way for new basophil activation methods to be explored. Methods Blood was collected from healthy subjects and patients with a history of allergy to food, drugs, house dust and grass pollen. Basophils were stimulated with specific allergen, anti-IgE antibody, or the peptide f-met-leu-phe (FMLP). Flow cytometry was performed with non-permeabilised and permeabilised cells with antibody specific for basogranulin (BB1) or CD63, and data analysed with CellQuest software. Results Flow cytometry with permeablised cells indicated depletion of intracellular stores of basogranulin following basophil activation. Associated with basogranulin release was the presence of increased quantities of this marker on the basophil membrane following cellular activation. Increased membrane expression of basogranulin mirrored that for CD63; and with allergens and other stimuli tested the measurement of cell surface basogranulin represented a more sensitive means for assessing basophil activation in vitro. The flow cytometric assays for basogranulin were optimised for use with samples of whole blood so as to avoid the need for basophil purification. Conclusions The rapidity, simplicity and sensitivity of basogranulin-based methods for measuring basophil activation will facilitate their application to clinical samples and allow better assessment for allergic sensitivity.