Background: JAK2mutation status is a well-known risk factor for thrombosis in patients with myeloproliferative neoplasms. However, the clinical usefulness of JAK2V617F allele burden is under investigation. Methods: We retrospectively evaluated the impact of the JAK2V617F allele burden on clinical characteristics and outcomes of JAK2V617F-positive polycythemia vera (PV) and essential thrombocythemia (ET). The JAK2V617F allele burden was measured using sequencing. Results: Altogether, 127 patients with JAK2V617F mutation (PV, N=61; ET, N=66) were included in this study. JAK2V617F allele burdens were positively correlated with white blood cell counts, hemoglobin values, lactate dehydrogenase levels, and platelet counts. The median values of JAK2V617F allele burden in patients with PV and ET were 58% and 30%, respectively. A JAK2V617F allele burden of ≥30%, older age, and a higher hemoglobin level were risk factors for thrombotic events in ET. In patients with PV, older age was the only thrombotic risk factor. The 8-year probabilities of overall survival (OS) were 82.9% in all patients. A high JAK2V617F allele burden (≥58%) was associated with poor OS in patients with PV. For the patients with ET, the difference in 8-year OS based on the JAK2V617F allele burden was not significant. Conclusion The JAK2V617F allele burden was correlated with hematologic parameters and clinical outcomes. Assessing the JAK2V617F allele burden can be helpful in predicting the thrombotic risk and disease course in patients with JAK2V617F-positive PV and ET.