Background The clinical significance of ascites in patients with extrahepatic portal vein thrombosis (EPVT) has been poorly defined. Aims To assess the frequency, natural history and prognostic implication of ascites in patients with EPVT and to identify risk factors for this complication. Methods A single-centre retrospective study of consecutive patients diagnosed with noncirrhotic nonmalignant EPVT between 1985 and 2009. Results One hundred and three patients [35% males; median age 43 (range 16-83) years] were included and followed up for a median time of 5.2 (range 0.9-32.5) years. Twenty-nine (28%) had ascites at the time of diagnosis. Overall survival was 91% at 5 years vs. 80% at 10 years. Survival in patients presenting with and without ascites was 83% vs. 95% at 5 years and 42% vs. 87% at 10 years (P = <0.01). There was no correlation between the presence of ascites and extension of the thrombus into the large splanchnic veins, duration of thrombosis or presence of gastrointestinal bleeding. Conclusions Ascites is present in a quarter of patients presenting with noncirrhotic nonmalignant extrahepatic portal vein thrombosis. Ascites is a significant and independent prognostic factor and it is associated with a decreased long-term survival.