The aim of this study was to determine the prevalence of venous thromboembolism (VT) in current prophylactic practice with low-molecular-weight heparin (LMWH) among medical inpatients and to analyze associated risk factors for VT. A cross-sectional survey on five given days was conducted in the medical departments of a university hospital. The prevalence of prophylaxis and confirmed VT was measured. Risk markers for receiving high doses of LMWH and for VT under prophylaxis were assessed by logistic regression models. Of 1,194 inpatients, 1.4% suffered VT. The mean proportion of patients with LMWH prophylaxis was 24% (range: 4-64%). The prevalence of VT was higher among inpatients receiving prophylaxis than among those patients not receiving prophylaxis (3.5% vs. 0.7%, p = 0.002). Under prophylaxis, independent risk markers for thrombosis were history of vein thrombosis (odds ratio [OR]: 4.03; confidence interval [95%CI]: 1.04-15.62) and age (OR: 1.08; 95%CI: 1.01-1.15). Two factors were independently associated with the prescription of high doses of LMWH: obesity was positively associated (OR: 7.50; 95%CI: 2.97-18.92; p < 0.0001) and respiratory insufficiency was negatively associated. In medical departments, current prophylaxis practice leads to many patients being given LMWH. LMWH doses and other preventive measures should be adapted in high-risk inpatients.