The Wells score had shown weak performance to determine pre-test probability of deep vein thrombosis (DVT) for inpatients. So, we evaluated the impact of thromboprophylaxis on the utility of the Wells score for risk stratification of inpatients with suspected DVT. This bicentric cross-sectional study from February 1, 2018 to January 31, 2019 included consecutive medical and surgical inpatients who underwent lower limb ultrasound study for suspected DVT. Wells score clinical predictors were assessed by both ordering and vascular physicians within 24 h after clinical suspicion of DVT. Primary outcome was the Wells score’s accuracy for pre-test risk stratification of suspected DVT, accounting for anticoagulation (AC) treatment (thromboprophylaxis for ⩾ 72 hours or long-term anticoagulation). We compared prevalence of proximal DVT among the low, moderate and high pre-test probability groups. The discrimination accuracy was defined as area under the receiver operating characteristics (ROC) curve. Of the 415 included patients, 30 (7.2%) had proximal DVT. Prevalence of proximal DVT was lower than expected in all pre-test probability groups. The prevalence in low, moderate and high pre-test probability groups was 0.0%, 3.1% and 8.2% ( p = 0.22) and 1.7%, 4.2% and 25.8% ( p < 0.001) for inpatients with or without AC, respectively. Area under ROC curves for discriminatory accuracy of the Wells score, for risk of proximal DVT with or without AC, was 0.72 and 0.88, respectively. The Wells score performed poorly for discrimination of risk for proximal DVT in hospitalized patients with AC but performed reasonably well among patients without AC; and showed low inter-rater reliability between physicians. ClinicalTrials.gov Identifier: NCT03784937.