The Gladomain of human factor IX contains a specific element required for the binding of factor IX to an endothelial cell surface protein. We have investigated the dependence of this interaction on the structural integrity of the adjacent hydrophobic stack and epidermal growth factor-like domains. The ability of purified natural variants of human factor IX to compete with wild-type factor IX binding to the endothelial cell surface was used to obtain apparent K i values of the variants. Our data suggest that the functional integrity of the Gla domain, enabling factor IX to specifically interact with an endothelial cell surface protein, depends on the structural and functional integrity of both the hydrophobic stack domain and the first epidermal growth factor-like domain.