Introduction Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal stem cell disease characterized by venous thrombosis and intravascular hemolysis, caused by a somatic mutation in the phosphatidylinositol N-acetylglucosaminyltransferase subunit A (PIGA) gene located on chromosome X [1-3]. PNH occurs with approximately equal incidence in men and women, and the overall disease prevalence has been estimated at 2-5 cases per 1,000,000. The mean age at onset of PNH is around 42 years, and the 5-year mortality rate is approximately 35% [4]. Clinically, PNH occurs in three different forms. Classic (hemolytic), bone marrow deficiency syndrome (hypoplastic), and a subclinical form [5]. Although the disease typically manifests with signs of bone marrow failure, thrombotic events, and chronic intravascular hemolytic anemia particularly those affecting the abdominal veins, are considered the most important complication during its course. Background/aim: Paroxysmal nocturnal hemoglobinuria (PNH) is a very rare clonal hematopoietic stem cell disease characterized by chronic hemolytic anemia and thrombosis. We report data from a study of the occurrence of PNH among patients with idiopathic portal vein thrombosis (PVT). Materials and methods: Patients who were followed up with the diagnosis of idiopathic PVT were enrolled into this study. Those with laboratory and/or imaging evidence of any local or systemic factor that could lead to PVT were excluded. PNH clone was examined in all patients using established FLAER methodology. Results: A total of 112 patients (42 males and 70 females), none of them had a markedly PNH clone, but 4 patients (3.6%) with confirmed tests two times had small PNH clones (size between 3.02% and 4.62%). The median ages of PNH clone (-) and PNH clone (+) patients were 42 (range; 24-59) vs 39 (range; 36-42) years, respectively. The median hemoglobin concentration, platelet count and leukocyte count were lower in the PNH clone (+) group than the PNH clone (-) group. Anemia, thrombocytopenia, and leukopenia were detected in all PNH clone (+) patients. In addition, the PNH clone positivity size in monocytes was higher than erythrocytes in all of 4 patients. Conclusions: PNH should be considered during differential diagnosis among patients with idiopathic PVT. Small PNH clones can be detected in PVT patients that we cannot clearly determine its relationship with PVT. We need furthermore studies to explore the potential role of this finding.