Factor IX Chicago-2 and prothrombin Madrid were purified from patients with hemophilia B and congenital dysprothrombinemia, respectively. Each protein displays defects in zymogen activation secondary to the failure to cleave one of the sessile bonds whose cleavage is necessary for full coagulant activity. These proteins were isolated by immunoaffinity chromatography using conformation-specific antibodies directed at either factor IX or prothrombin. Factor IX Chicago-2 is cleaved abnormally by factor XIa, yielding a pattern consistent with the failure to cleave the sessile bond between Arg 145 and Ala 146. Prothrombin Madrid is cleaved abnormally by factor Xa, yielding a pattern consistent with the failure to cleave the sessile bond between Arg 271 and Thr 272. Peptide mapping was performed on reduced and alkylated factor IX, factor IX Chicago-2, prothrombin, and prothrombin Madrid, and the hydrolysates were separated by high-performance liquid chromatography. The mutant peptide in factor IX Chicago-2 was identified by automated Edman degradation as residues 143 through 188 of factor IX, and had a histidine substituted for arginine at residue 145. The mutant peptide identified in prothrombin Madrid corresponds to residues 267 through 285 of prothrombin and has the substitution of cysteine for arginine at residue 271. These mutations, each occurring at arginines, are identical to those in factor IX Chapel Hill and prothrombin Barcelona. These results suggest that a limited repertoire of point mutations, many affecting arginine residues, may be responsible for hereditary defects of the vitamin K-dependent proteins in patients with normal antigen levels.