Three male German Shepherd Dog pups were treated for vaccination-induced hematomas. Coagulation tests in 2 of these pups revealed markedly prolonged activated partial thromboplastin times, whereas specific coagulation factor tests revealed severe deficiency of factor IX activity. Investigation of the pedigree supported a sex-linked pattern of inheritance and a distant relationship to a pup found to have hemophilia B 7 years earlier. Dogs in the pedigree had variable manifestations of bleeding, including hematomas, deep muscle bleeding, profuse bloody diarrhea, and sudden neonatal deaths. von Willebrand's disease was concurrently detected in several dogs in the pedigree, and may have contributed to the bleeding tendency in some dogs. Medical management of 2 of the 3 pups included transfusion of fresh whole blood, canine fresh-frozen plasma, and canine plasma cryosupernatant, as indicated, and cage rest. Two pups were euthanatized because of the severity of recurrent bleeding episodes. A third dog remains alive, but requires periodic infusions of blood product to maintain hemostasis.