Introduction: Critical care patients are at higher risk for thromboembolic disorders. There are limited studies regarding the effect of Heparin, Warfarin, Enoxaparin and Aspirin on ventilated patients, who are likely to both benefit from prophylaxis and suffer from adverse effects of blood thinners. Methods: This study analyzed the MIMIC-III clinical database on 4192 ventilated patients using Statistical Analysis Software (SAS, Version 9.4). Relevant data was systematically analyzed on the thromboprophylaxis agents and their effects on major treatment outcomes. Parameters studied were the length of ventilation, length of Intensive Care Unit (ICU) stays, ICU mortality, inpatient mortality, improvement in SOFA score, and occurrence of major thromboembolic events such as pulmonary embolism (PE) and deep venous thrombosis (DVT). Results: Except Aspirin, all thromboprophylactic agents showed statistically significant reduction on ICU mortality. None of the blood thinners showed statistically significant reduction in occurrences of pulmonary embolism and deep venous thrombosis. Heparin, Warfarin and Enoxaparin had adjusted Odds ratios of 0.59(p<0.01, 0.47-0.77), 0.23(p<0.05, 0.1-0.57) and 0.36(P<0.05, 0.16-0.83) for ICU mortality. Heparin, Warfarin and Enoxaparin had adjusted Odds ratios of 0.51(p<0.01, 0.38-0.68), 0.19(p<0.01, 0.06-0.59) and 0.42(P=0.06, 0.17-1.05) for overall ventilated patient hospital mortality, including after transfers to the inpatient ward.. Only Heparin (P<0.05, OR 1.52(1.07-2.15)) was associated with thrombocytopenia episodes, which required platelets transfusion. None of the drugs showed statistically significant relationships with development of thromboembolic events after thromboprophylaxis. Only Heparin had mild effect on improvement in sequential organ failure assessment (delta SOFA) scores at 7 and 10 day after ICU admission (P<0.05, OR 1.17 (1.03-1.32)). Conclusion: Although the results supported the use of thromboprophylaxis in ventilated patients to improve treatment outcomes and decrease thromboembolic events, no benefits were indicated for using newer blood thinners (Enoxaparin) than older ones (Heparin & Warfarin). The results of this analysis might help practitioners select, maintain, and switch blood thinners in ventilated patients.