Approximately half of the patients with essential thrombocythaemia (ET) harbor the JAK2 V617F mutation. Despite a phenotypic mimicry of JAK2 V617F positive ET and polycythaemia vera (PV), the data on thromboembolic risk and correlation to JAK2 mutation status are ambiguous. On a strictly WHO defined ET cohort we evaluated possible clinical correlations to the JAK2 mutation status including a history of previous thrombosis. We used a highly sensitive quantitative real-time PCR (qPCR) assay for JAK2 V617F detection and allele burden quantification in a single institution study of 55 patients. A significantly increased prevalence of arterial thrombosis was recorded in JAK2 positive ET (p=0.001). There was no association between the mutational load and thrombosis. As compared to their JAK2 V617F negative counterparts, the JAK2 V617F positive patients had PV-like biochemical characteristics such as higher haemoglobin levels (p=0.02), lower platelet counts (p=0.002) and lower plasma EPO levels (p=0.04). The JAK2 V617F mutation per se but not the mutational load in patients with ET is associated with a PV-like phenotype and a higher prevalence of previous arterial thrombosis. This study adds further support to the contention of the JAK2 V617F mutation as a marker of increased risk of thrombosis.