Blood clotting factor IX is synthesized as a precursor polypeptide that would be expected to be proteolytically cleaved in at least two positions during maturation to remove the prepeptide and propeptide regions. We show that a point mutation causing hemophilia B changes the amino acid at position -4 in the propeptide region of factor IX from an arginine to a glutamine, which results in the expression of a stable longer protein with 18 additional amino acids of the N-terminal propeptide region still attached. This suggests that in the normal maturation of factor IX the signal peptidase cleaves the peptide bond between amino acid residues -18 and -19, generating an unstable profactor IX intermediate. Further proteolytic processing to the mature factor IX depends on the arginine residue at -4. The significance of the homologous arginine residue in other processed proteins is discussed.