BACKGROUND. Hemophilia B is X-linked recessive genetic disorder, caused by missing or defective factor IX that results in bleeding longer after an injury or surgery, easy bruising, and an increased risk of bleeding inside joints or the brain. The disorder affects approximately one in 30 000 males worldwide and 18 cases were registered in Mongolia according to statistics of Hemophillia Federation of Mongolia. The annual cost of episodic treatment of an adult with severe hemophilia estimated at ≈53000 USD owing to high cost of treatment developing countries has been adopted to prevent and to forecast the risk of inhibitor. Materials and Methods: The objective of this research is to determine F9 mutations in patients with Hemophillia B in Mongolian population and to assess correlation between genotype and phenotype of disease. Characterization of mutations was performed by direct sequencing of genomic DNA using a Sanger sequencing method. Briefly, the exon or part of the exon deletion was checked and amplified by polymerase chain reaction (PCR). Results: We identified four point mutations and one deletion. No large exon deletion was found in PCR amplification result. As expected, the most common mutations responsible for the disease were point mutations. In general, this study revealed 5 different mutations in unrelated 7 proband and there is good correlation between the type of mutation (location in the amino acid position and domain in the protein) and their functional outcome, yielding a predictable clinical severity.