BACKGROUND:Both unfractionated heparin (UFH) and low‐molecular‐weight heparin (LMWH) are approved for venous thromboembolism (VTE) prophylaxis. Which agent is superior remains controversial.OBJECTIVE:To compare the effectiveness, complications, and costs of UFH and LMWH as VTE prophylaxis for hospitalized medical patients.DESIGN:Retrospective cohort.SETTING:Three hundred thirty‐three acute care facilities in 2004–2005.PATIENTS:Adults with 4 common medical diagnoses considered to carry moderate‐to‐high risk of VTE. Excluded were patients on warfarin or with hospital stays of ≤2 days. VTE prophylaxis was assessed from billing data.INTERVENTION:None.MEASUREMENTS:VTE, major bleeding or heparin‐induced thrombocytopenia, mortality, and cost.RESULTS:Of 32,104 patients who received prophylaxis, 55% received LMWH and the remainder received UFH. The hospital where the patient obtained care was the strongest predictor of receiving LMWH. VTE was observed in 163 (0.51%) patients; complications, followed by stopping therapy, were rare (<0.2%). In analysis adjusted for the propensity for UFH and other covariates, patients treated with UFH had an odds ratio for VTE of 1.04 (95% confidence interval [CI] 0.76 to 1.43) compared to LMWH. In a grouped treatment model, the odds of VTE with UFH was 1.14 (95% CI 0.72 to 1.81). Adjusted odds of bleeding with UFH compared to LMWH were 1.64 (95% CI 0.50 to 5.33), adjusted odds of complications followed by stopping prophylaxis were 2.84 (95% CI 1.43 to 45.66), and adjusted cost ratio was 0.97 (95% CI 0.90 to 1.05).CONCLUSIONS:For VTE prophylaxis, the effectiveness and cost of LMWH and UFH are similar, but LMWH is associated with fewer complications. Journal of Hospital Medicine 2012;. © 2012 Society of Hospital Medicine