The latest developments in emergency medicine (EM) have introduced new typologies of patients that have not been taken into account in previous studies of venous thromboembolism (VTE) risk. The aim of the current study was to evaluate by comparing the main international risk scores whether different perceptions of VTE risk exist in internal medicine (IM) departments and in EM departments. This cross-sectional observational study involved 23 IM and 10 EM departments of 21 different hospitals. The patient data were collected by physicians who were blinded to the purpose of the study. The data were analyzed using the main international risk scores. We analyzed 742 patients, 222 (30%) hospitalized in EM departments and the remaining 520 (70%) in IM departments. We found that fewer patients at risk for VTE were treated with low-molecular-weight heparin (LMWH) in EM departments than in IM departments. Moreover, there was significant statistical difference in the use of LMWH between IM and EM departments when the Padua score and immobilization criteria were used to assess the risk. The infrequent use of LMWH in EM patients may have several causes. For example, in EM departments, treatment of acute illness often takes higher priority than VTE risk evaluation. Moreover, immobilization criteria cannot be evaluated for all EM patients because of the intrinsic time requirements. For the aforementioned reasons, we believe that a different VTE risk score is required that takes into account the peculiarities of EM, and establishing such a score should be the object of future study.