Hemophilia B is a hereditary disease linked to chromosome X and consists in the deficiency of factor IX blood clotting. This hemorrhagic disease affects one in 30,000 men worldwide. The level of biologically active Factor IX in the patients' plasma is directly related to the severity and frequency of bleeding episodes. Since the advent of recombinant DNA technology, it was feasible to clone the gene for factor IX, which made possible its molecular characterization. Knowledge of the molecular basis of hemophilia B has allowed a better understanding of the relationships between factor IX gene structure and active Factor IX protein function. The existing treatment is given by biological replacement therapy, through intravenous infusions of Factor IX derived from human plasma or recombinant Factor IX. This article aims to summarize the knowledge about the molecular basis of hemophilia B (gene, RNA, and protein), the cascade of blood clotting, the process of development of recombinant Factor IX and the situation in worldwide and Brazil in face of the current treatment and the future prospects of hemophilia B.