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Background: Although venous thromboembolism is an important cause of morbidity and mortality within the hospital, a significant proportion of at-risk inpatients do not receive measures known to reduce the risk of deep vein thrombosis and pulmonary embolism. Objective: To determine whether a pharmacy driven alert system would, compared to usual care, be associated with a higher rate of adequate VTE prevention measures among at-risk inpatients on a general internal medicine service. Design: Prospective, controlled trial. Setting: A university-based teaching hospital. Patients: Adults admitted (Monday through Friday) to the general internal medicine inpatient service from 6/19/06-9/21/06. Intervention: Pharmacist assessment of venous thromboembolism risk; pharmacist-driven alert to treating physician. Measurements: Proportion of at-risk patients receiving adequate thromboprophylaxis within 36 hours of admission. Results: Overall, 140 patients were at sufficient risk for VTE to be included. In the usual care group, prophylactic measures were ordered for 49 (61%) of the 80 patients at moderate to high risk. In the pharmacist-alert group, 44 (73%) of the 60 moderate to high VTE risk patients received adequate thromboprophylaxis (p = 0.15). Conclusions: Although we did not observe a statistically significant difference between the experimental groups, our results are consistent with previous reports suggesting that alert systems (whether computerized or human) can increase the proportion of hospitalized patients who receive adequate measures to prevent VTE.