Factor IX is a vitamin K dependent plasma proteinsynthesized in the liver; a deficiency of Factor IX results in hemophilia B. An animal model for hemophilia B exists in dogs; affected animals have severe disease, with activity levels of less than 1%. The purpose of the current study is to determine the molecular basis of canine hemophilia. In previous work, we had shown that the Factor IX gene in hemophilic dogs appeared to be at least partly intact; thus, genomic DNA from normal, carrier and hemophilic dogs, when probed with sequences from the 4th, 7th, and 8th exons of the human gene, gave identical patterns on Southern blot. We have now completed the mapping of the hemophilic gene, using probes from the first, second, third and sixth exons, and have shown it to beentirely intact, that is, free of any large deletions or rearrangements, as determined by Southern blotting. In addition, using the guanidinium thiocyanate technique, we h^ve prepared total RNA from normal and -hemophilic dog livers add analyzed these samples by Northern blotting. The results show that the hemophilic dog synthesizes a Factor IX transcript of approximately 3 kilobases, that is, of the same size asthe normal dog. In addition, baaed on signal intensity, the transcript appears to be produced in roughlyequivalent amounts in the normal and hemophilic dogs.We conclude that the defect responsible for canine hemophilia B interferes with the production of the normal Factor IX protein at a post-transcriptional level. Moreover, since the hemophilic dogs produce Factor IX mRNA it should be possible to elucidate the gene defect in the hemophilic animals by preparing normal and hemophilic canine liver cDNA libraries and isolating and characterizing the respective Factor IX cDNAs.