The investigation of anaphylactic reactions in the peri-operative period is difficult. Elevation of serum tryptase levels is a good indicator of an anaphylactic event but the ability of subsequent investigations to identify the drug(s) responsible for the reaction is still potentially unreliable. The aim of this study was to examine basophil activation as an investigative tool. We performed flow cytometric analysis of the expression on the cell surface of the basophil activation markers CD63 and CD203c and measured histamine release in 21 patients who were referred with possible peri-operative anaphylaxis. The sensitivity of CD63, CD203c, basophil histamine release and skin prick for the muscle relaxants was found to be 79%, 36%, 36% and 64%, respectively; the specificity was found to be 100%. These results demonstrate the difficulty in investigating the cause of an unexpected clinical event following drug administration, but the higher sensitivity of neo-expression on the cell surface of CD63 suggests that flow cytometric analysis of its neo-expression on basophils in vitro may be a diagnostic aid.