Introduction: The risk of venous thromboembolism (VTE) is increased by more than 100-fold among hospitalised medical patients compared to subjects in the community. The Danish Council for the Use of Expensive Hospital Medicines has published national guidelines on thromboprophylaxis (TP) in which the risks of VTE and bleeding are balanced. We wanted to investigate the proportion of acutely admitted medical patients for whom thromboprophylaxis was indicated and to what extent the guidelines were followed. Methods: Data from patients hospitalised at two medical wards were screened. We registered the proportion of patients for whom mechanical or pharmacologic TP (MTP and PTP, respectively) was indicated and whether national guidelines were followed. All data extraction and analyses were performed retrospectively. Results: After exclusion criteria were applied, 340 cases remained. PTP was indicated in 26 patients (7.6%) but only 4 patients were treated besides 12 patients who were already in anticoagulant treatment at submission. Conversely, 8/306 patients, in whom TP was not indicated, were started on PTP. MTP was indicated in 8/340 patients (2.4%) but therapy was not initiated in any of them. The majority (320/340, 94.1%) of cases was managed in accordance with existing guidelines. However, this high proportion was mainly explained by the large number of untreated patients, where TP was not indicated. Conclusion: A large proportion of hospitalised medical patients was managed in conflict with national guidelines. A systematic approach to TP in patients with acute medical illness should be implemented. Plain Language Summary: Plain language summary available for this article.