Thrombosis is the most important underlying mechanism of coronary artery disease and embolic stroke. Hence, antithrombotic therapy is widely used in these scenarios. However, not all patients achieve the same degree of benefit from antithrombotic agents, and a considerable number of treated patients will continue to experience a new thrombotic event. Such lack of clinical benefit may be related to a wide variability of responses to antithrombotic treatment among individuals (i.e., interindividual heterogeneity). Several factors have been identified in this interindividual heterogeneity in response to antithrombotic treatment. Pharmacogenetics has emerged as a field that identifies specific gene variants able to explain the variability in patient response to a given drug. Polymorphisms affecting the disposition, metabolism, transporters, or targets of a drug all can be implicated in the modification of an individual's antithrombotic drug response and therefore the safety and efficacy of the aforementioned drug. The present paper reviews the modulating role of different polymorphisms on individuals' responses to antithrombotic drugs commonly used in clinical practice.