Anticoagulation for the prevention of stroke is an important aspect of the management of atrial fibrillation. Novel anticoagulants including oral factor Xa inhibitors rivaroxaban and apixaban and the direct thrombin inhibitor dabigatran have emerged as important therapeutic treatment options for prevention of stroke in non-valvular atrial fibrillation. These agents offer practical advantages over traditional vitamin K antagonists, however an understanding of their individual pharmacokinetic and other agent-specific differences is essential for identifying appropriate candidates for therapy, and for selecting the appropriate agent that will be effective and safe. Here, we review the pharmacokinetic process of oral medication use, summarize the newer anticoagulants, their pharmacology, individual pharmacokinetic features, and explore possible explanations for the differences in bleeding outcomes observed in the clinical trials.