The formation of alloantibodies against factor VIII (FVIII) or factor IX (FIX) is the most severe complication of replacement therapy in patients with haemophilia. In the last decade, genetic factors have been shown to constitute a decisive risk determinant for the development of inhibitors. In severe haemophilia A and B, mutations that result in an absent or truncated FVIII/FIX protein are associated with a 20-80% risk of inhibitor formation. In mild to moderate haemophilia, missense mutations represent the main mutation type, with an inhibitor prevalence of 5%. These patients synthesize some endogenous, although non-functional protein that is sufficient to induce immune tolerance. However, in patients with missense mutations clustered in the A2 and C2 domains (C1/C2 junction), the risk of inhibitor formation is fourfold greater than in patients with mutations outside this region, indicating that inhibitor prevalence in missense mutations is also dependent on localization of the mutation. Recently, a significant association between inhibitor formation and polymorphisms in genes coding for cytokines (IL-10) and other immunoregulatory factors (TNF-alpha) has been shown. These genetic factors constitute the individual genetic risk profile of a haemophilic patient. This risk is imprinted and fixed; however, environmental factors such as treatment schedule may increase or decrease the inhibitor risk in an individual patient. Improved understanding of these complex interactions may lead to the development of preventive measures to minimize inhibitor formation.