BACKGROUND: The adequacy of thromboprophylaxis prescriptions in acutely ill hospitalized medical patients needs improvement. OBJECTIVE: To prospectively assess the efficacy of thromboprophylaxis adequacy of various clinical decision support systems (CDSS) with the aim of increasing the use of explicit criteria for thromboprophylaxis prescription in nine Swiss medical services. METHODS: We randomly assigned medical services to a pocket digital assistant program (PDA), pocket cards (PC) and no CDSS (controls). In centers using an electronic chart, an e-alert system (eAlerts) was developed. After 4 months, we compared post-CDSS with baseline thromboprophylaxis adequacy for the various CDSS and control groups. RESULTS: Overall, 1085 patients were included (395 controls, 196 PC, 168 PDA, 326 eAlerts), 651 pre- and 434 post-CDSS implementation: 472 (43.5%) presented a risk of VTE justifying thromboprophylaxis (31.8% pre, 61.1% post) and 556 (51.2%) received thromboprophylaxis (54.2% pre, 46.8% post). The overall adequacy (% patients with adequate prescription) of pre- and post-CDSS implementation was 56.2 and 50.7 for controls (P = 0.29), 67.3 and 45.3 for PC (P = 0.002), 66.0 and 64.9 for PDA (P = 0.99), 50.5 and 56.2 for eAlerts (P = 0.37), respectively, eAlerts limited overprescription (56% pre, 31% post, P = 0.01). CONCLUSION: While pocket cards and handhelds did not improve thromboprophylaxis adequacy, eAlerts had a modest effect, particularly on the reduction of overprescription. This effect only partially contributes to the improvement of patient safety and more work is needed towards institution-tailored tools.