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A higher rate of postoperative morbidity and mortality in patients with portal hypertension from cirrhosis is well recognized; however, the rate of postoperative morbidity and mortality among patients with portal hypertension from non-cirrhotic portal vein thrombosis (NCPVT) is largely unknown. All adults undergoing abdominal and pelvic surgery were identified from the National Inpatient Sample database from 2002 to 2015. Patients were then categorized into three groups: non-cirrhotic non-portal vein thrombosis (NCNPVT), NCPVT, and cirrhotic portal vein thrombosis (CPVT). Inpatient mortality, type of disposition, transfusions, length of stay, postoperative complications, and total charges were compared. Logistic regression and ordinary least squares regression analyses were performed for factors associated with inpatient mortality, transfusions, surgery-related complications, and log length of stay. Patients with NCPVT had significantly higher inpatient mortality rates, surgery-related complications, and longer length of stays compared with patients with NCNPVT (2.64% vs. 0.34%, 10.26% vs. 3.26%, 8 vs. 2 days) but less than patients with CPVT (2.64% vs. 6.31%, 10.26% vs. 17.48%, 8 vs. 11 days). In multiple logistic regression analyses, NCPVT groups remained associated with increased inpatient mortality rate, transfusions, and postoperative complications with odds ratios of 3.71 (1.88, 7.32), 3.43 (2.54, 4.62), and 3.08 (2.16, 4.39), respectively. NCPVT was also associated with 2.4 times increased length of stay. Patients with NCPVT had significantly higher risks of postoperative morbidity and mortality than patients with NCNPVT but less than patients with CPVT. Future studies with detail regarding the characteristics of PVTs are needed to confirm the findings in this study.