Background The clinicopathological features and long-term outcomes of vanishing bile duct syndrome (VBDS) remains to be revealed. The aim of this study was to elucidate the clinicopathological features and identify potential factors for poor prognosis in patients with VBDS.Methods This retrospective study recruited patients with liver biopsy-proven VBDS who were followed up at five hospitals in northern China from January 2003 to April 2022. Clinical and pathological data at time of biopsy were reviewed. Clinical outcomes including development of cirrhosis, decompensation events, liver transplantation (LT) or liver-related death were recorded. Cox regression analysis was used to identify risk factors in the prediction of dismal outcomes.Results A total of 183 patients were finally included. The median age at the diagnosis was 47 (38, 55) years, with 77.6% being women. During a median follow-up time of 4.8 years, 48.1% of the patients developed compensated or decompensated cirrhosis, with 27 die and 15 received liver transplantation. Multivariate Cox regression analysis showed that hepatocellular cholestasis (HR 2.953, 95%CI 1.437-6.069), foam cells (HR 2.349, 95%CI 1.092-5.053), and advanced fibrosis (HR 2.524, 95%CI 1.313-4.851) were independent predictors for LT or liver-related deaths. A nomogram formulated with the above factors showed good consistency with concordance index of 0.746 (95% CI 0.706-0.785). Conclusions Nearly half of the patients with VBDS progressed to end-stage liver disease and 23% of them had LT or liver-related death within two years after diagnosis. Histological factors including hepatocellular cholestasis, foam cells and advanced fibrosis were independently associated with poor prognosis in patients with VBDS.