Immunophenotyping of haematological malignancies has developed as a clinically valuable but technically complicated diagnostic procedure. It involves a variety of methodological features, in-process strategic judgements and an extensive knowledge of clinical, morphological and other laboratory features of the disease processes under study. We discuss the various internal quality control steps necessary to guarantee reliable results with respect to instrument set-up and calibration; sample preparation; selection and validation of monoclonal antibody panels; and flow cytometric data acquisition, analysis and interpretation of results. The quality of the entire procedure is documented by the analysis of representative specimens in the setting of an external quality assurance programme.