The role of platelet activation in clinical settings is controversial, partly because the methods used to detect platelet activation (e.g. platelet aggregation and radioimmunoassays of plasma β-thromboglobulin and platelet factor 4) are plagued by major methodological problems. Clinical studies that utilize flow cytometric assays of washed platelets are also susceptible to artefactual in vitro platelet activation. Whole blood flow cytometry circumvents many of these methodological problems. However, a major limitation in previously described whole blood flow cytometric assays is their inability to study the effect on platelet activation of thrombin, the most important platelet agonist in vivo. This article reviews the method and clinical applications of a new flow cytometric assay in which platelet activation by thrombin is directly measured in whole blood through the use of the peptide Gly-Pro-Arg-Pro (GPRP). GPRP inhibits thrombin-induced fibrin clot formation and platelet aggregation, but not thrombin-induced platelet activation. The presently described assay of platelet activation by thrombin in the physiological milieu of whole blood should be widely applicable to the many clinical settings (e.g. arterial thrombosis) in which platelet activation by thrombin is postulated to play an important role.