In neonates and infants, numerous clinical and environmental conditions lead to elevated thrombin generation and subsequent thrombus formation. Genetic prothrombotic defects (protein C, protein S and antithrombin deficiency, mutations of coagulation factor V and factor II, elevated lipoprotein (a)) have been established as risk factors of thromboembolic events in neonates and infants. The interpretation of the laboratory evaluation relies on age-dependent normal reference values. Because appropriate clinical trials are missing in these age groups, treatment recommendations are adapted from small-scale studies in neonates and infants and from guidelines relating to adult patient protocols. Secondary long-term anticoagulation should be administered on an individual basis.