Following the recommendations of the European Group for the Immunological Characterization of Leukaemias (EGIL) in 1995, few reports have been published comparing enzyme cytochemistry (EC) and flow cytometry (FC) for the detection of myeloperoxydase (MPO) in acute myeloid leukaemia (AML). The EGIL guidelines defined MPO positivity in FC, by the presence of this enzyme in 10% or more of the blast cells. We studied 136 adult patients with the systematic use of both EC and FC, using a 3% threshold for positivity for EC, and 10% and 3% consecutively for FC. FC was less sensitive than EC using the currently recommended threshold of 10%, but a 3% cut-off showed more sensitivity and was superior to EC. The joint use of both techniques identified 14 discordant patients (positive in FC/negative in EC or vice versa), all of whom displayed at least one poor-prognosis biological factor, which correlated with a mediocre clinical result. In conclusion, we recommend that the cut-off for a positive MPO value should be lowered to 3%, and suggest that the concomitant use of FC and EC is a fast clinically relevant prognostic tool.