Aptamer molecules represent an attractive approach in pharmacological therapy. Thrombin is a plasma serine protease that plays a key role in coagulation and haemostasis, also playing a relevant role in endothelial and smooth muscle cell functions. Thus, the development and use of direct thrombin inhibitors represents a potent tool in cardiovascular therapeutics. This review describes the status of direct thrombin inhibitors, focusing on aptamer-based drug candidates, that are at present in pre-clinical and in clinical trials. In addition, more recent research strategies in the design of novel aptamer thrombin inhibitors are presented and discussed. In particular, their structural, conformational, pharmacokinetic and pharmacodynamic properties are discussed in relation with the specificity of their binding to relevant thrombin exosites, which regulate the enzyme interaction with natural substrates and cellular receptors. Despite the addition of new effective anticoagulants to the therapeutic armoury, there remains a need for safer and effective anticoagulants. The aptamer- based thrombin inhibitors may represent an attractive approach for future developments of more potent and safer anticoagulants.