Background Portal vein thrombosis (PVT) is common in patients with cirrhosis, but the risk factors associated with PVT and its impact on outcomes following liver transplantation (LT) are not well defined. The objectives of this study were to determine the impact of PVT on post-LT patient and graft survival, waitlist outcomes, and the factors associated with PVT. Methods A retrospective review of Organ Procurement and Transplant Network waitlist and LT data between 2002 and 2013 identified 48,570 patients undergoing their first LT, with 3321 (6.8%) reported to have PVT at LT. Results Portal vein thrombosis was independently associated with increased 90-day mortality (odds ratio, 1.7; 95% confidence interval, 1.45-1.99; P < 0.001) and graft failure (odds ratio, 1.72; 95% confidence interval, 1.51-1.97; P < 0.001). Portal vein thrombosis at listing was not associated with lower transplant rates, or delisting for death, or deterioration. Only 31% of patients with PVT at LT had PVT reported at listing. The predictors of PVT at LT in patients without PVT at listing included: fatty or cryptogenic liver disease, ascites, diabetes mellitus, and obesity. New PVT at LT was associated with longer wait-time, higher rate of model of end-stage liver disease increase, and intermediate 90-day survival rates compared to patients with or without PVT at both listing and LT. Conclusions Portal vein thrombosis at LT is associated with early (90 days) mortality and graft failure, though a likely but undefined reporting bias for more extensive PVT would overstate estimated risks for all PVT. Further study is needed to better define risks of LT with PVT.