Hemophilia B is a heritable bleeding disorder caused by mutations in the gene coding for coagulation factor IX. The defect has been identified in purebred and mixed-breed dogs. Management of affected dogs requires transfusion of canine blood products supplying active factor IX. Production of inhibitors to factor IX is a complication of transfusion therapy that has been documented as affecting human patients. Risk for producing coagulation inhibitors is greatest for patients having large factor IX gene deletions. To our knowledge, this is the first report of canine factor IX inhibitor production in dogs. The affected dog had clinically severe hemophilia B caused by complete deletion of the factor IX gene and developed resistance to transfusion. Comprehensive evaluation of hemophilic dogs, including assays of specific factor activity, concentration, and factor inhibition, enhances diagnosis and management of this bleeding disorder. Characterization of the molecular defect causing hemophilia is useful for genetic counseling and identifying individuals at highest risk for producing coagulation inhibitors.