Myeloproliferative neoplasms (MPN) are the most frequent cause of non-tumoral non-cirrhotic splanchnic vein thrombosis (NC-SVT). Diagnosis of MPN is based on blood cell count alterations, bone marrow histology and detection of specific gene mutations. Next generation sequencing (NGS) allows the simultaneous evaluation of multiple genes implicated in myeloid clonal pathology. The aim of this study was to evaluate the potential role of NGS in the etiology of NC-SVT.DNA samples from 80 patients, (75 with idiopathic or exclusively local factor (Idiop/loc-NC-SVT) and 5 with MPN and NC-SVT (SVT-MPN) negative for JAK2 (V617F and exon 12), CALR and MPL mutations by classic techniques) were analyzed by NGS. Mutations involved in myeloid disorders different from JAK2, CALR and MPL genes were categorized as High Molecular Risk (HMR)-variants or Variants of Unknown Significance (VUS).In 2/5 triple-negative SVT-MPN cases (40%) a mutation in exon 12 of JAK2 was identified. JAK2-exon 12 mutation was also identified in 1/75 patients with idiop/loc-NC-SVT. Moreover, 28/74 (37.8%) of the remaining idiop/loc-NC-SVT had at least one HMR variant. Sixty-two patients with idiop/loc-NC-SVT were not receiving long-term anticoagulation and five of them (8.1%) had recurrent NC-SVT. This cumulative incidence was significantly higher in patients with HMR-variants than in those without.NGS identified JAK2-exon12 mutations not previously detected by conventional techniques. In addition, NGS detected HMR-variants in approximately one third of patients with idiop/loc-NC-SVT. These patients seem to have a higher risk of splanchnic rethrombosis. NGS might be a useful diagnostic tool in NC-SVT.