The invention provides a method of treating bleeding disorders in a subject by administration of a preparation enriched for Factor IXa. The Factor IXa can be produced by proteolytically activating recombinantly-produced Factor IX. The invention also provides an improved method for producing Factor IXa from a plasma fraction, which method results in a Factor IXa product containing little or no prekallikrein activity, thus reducing the incidence of undesired side effects in a subject.