The molecular characterization of myeloproliferative neoplasms, including essential thrombocythemia (ET), has enabled deeper understanding of their pathogenesis. A driver lesion, namely, Janus kinase (JAK)2V617F, calreticulin (CALR) or myeloproliferative leukemia (MPL) gene mutation can be identified in the vast majority of patients. Each of these mutations is associated with distinct clinical features and may modulate the patients' clinical course, risk of complications, including vascular events, and survival. JAK2V617F appears to be a risk-modifying mutation and has been shown to increase the likelihood of thrombotic events in patients with ET across studies. As such, it has been included in prognostic models and its presence may influence treatment decisions. The association of CALR and MPL mutations with the incidence of vascular events has been less clear. Even more limited information is available on the contribution of additional non-driver lesions to the thrombotic risk. In this review we discuss the available evidence on the role of recurrent mutations in the risk of thrombotic complications in patients with ET and how these mutations weigh into modern prognostic scores.