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Abstract Budd-Chiari syndrome (BCS) is a rare disorder caused by obstruction of the hepatic veins or the suprahepatic inferior vena cava. Myeloproliferative diseases (MPD) are the most important aetiological factor in BCS. The aim of this study was to evaluate multifactorial aetiology in BCS patients with MPD, to assess potential added value of the recently discovered JAK2 mutation in the diagnostics of MPD in BCS, and to determine the survival of MPD patients in BCS. All patients referred to our university hospital with primary, non-malignant BCS between January 1980 and January 2006 were included in this study (n=40). Median age was 28.4 years (18.4–53.3), 26 patients (65%) were female and in nine patients (23%) additional portal vein thrombosis (PVT) was present. Overall mean follow-up was 7.1 ± 6.9 years. Only two patients were lost to follow-up, of which one MPD patient. In addition to standard MPD work-up according to WHO criteria, JAK2 mutation analysis was performed in 17 patients. MPD was present in 33% of the patients: Polycythemia Vera (n=6), Essential Thrombocythemia (ET) (n=6) and unclassifiable MPD (n=1). JAK2 mutation was identified in seven out of the 17 tested BCS patients (41%). In two patients suspect for ET, but who failed to meet WHO criteria, JAK2 mutation analysis led to the diagnosis of MPD. In 38% of patients with MPD additional pro-thrombotic factors were present. Survival rates in patients with MPD at 1, 5, and 10 years remained constant at 92% (95% CI, 78%–100%). Survival rates in patients without MPD at 1, 5, and 10 years were 89% (95% CI, 77%–100%), 64% (95% CI, 44%–85%) and 53% (95% CI, 28%–79%), respectively. There was no significant difference in survival between the two (P=0.18). Additional PVT was only present in patients without MPD in our population, which may account for the slightly lowered survival of these patients, since more extensive thrombosis in the splanchnic area is associated with poorer survival. In addition, three patients with and one patients without MPD underwent liver transplantation, which may have affected survival rate in favour of MPD patients. In conclusion, we report MPD in 33% of our BCS patients. In 38% of the patients with MPD, additional pro-thrombotic factors were present. These results enforce the necessity of extensive screening for additional pro-thrombotic conditions. Our study clearly confirms the importance of JAK2 mutation analysis in patients with BCS. Long term follow-up did not show a significant difference in survival between patients with and without MPD.