Although the primary aim of the treatment of primary thrombocythaemia is to reduce platelet counts, its effect on platelet activation, vascular dysfunction and coagulopathy, which are also abnormal, is unknown. We therefore hypothesised that successful treatment of primary thrombocythaemia is accompanied by an improvement in markers of these processes. To test this hypothesis, we compared 38 patients with 15 healthy age and sex-matched controls. Seven untreated patients had platelet counts higher than those 31 on treatment, that were in turn higher than the 15 controls (all p < 0.01). Plasma fibrinogen, P-selectin, von Willebrand factor and sVCAM were higher in both patient groups compared to controls (all p < 0.05), but not between patient groups. sE-selectin and sICAM were unaltered between the three groups. D-dimers were higher in treated patients than in controls. We conclude that successful thrombocytosis treatment does not normalise markers of coagulation, platelet, or endothelial pathophysiology. This may account for continuing risk of pathology in those whose platelet counts have been normatised.