Background and Objectives: Hemophilia B, Christmas disease, is an X-linked recessive bleeding disorder caused by the functional deficiency of blood coagulation factor IX (FIX). The disease is caused by heterogeneous mutations in the factor IX gene (factor IX). FIX is a vitamin K-dependent glycoprotein that plays a key role in the coagulation cascade. The aim of this study was to make molecular analysis of factor IX gene and evaluate genotype-phenotype correlation in 14 hemophilia B patients from Khorasan Razavi province. Materials and Methods: Fourteen unrelated hemophilia B patients were included in the study. The patients had high PTT, normal PT, low factor IX activity (less than 30%), and normal FVIII activity. After obtaining informed consent, genomic DNA was extracted from the peripheral blood leukocytes by standard methods. Polymerase chain reaction (PCR) and single strand conformation polymorphism (SSCP) were performed to obtain a full scan of all functionally important regions of the FIX gene. DNA sequencing was done on samples with a definite band shift in SSCP. In addition, Haplotypes were constructed using four markers (DdeI, TaqI, MnlI and HhaI).Results: The sequencing results showed 9 missenes mutations, 3 stop codons, and 1 insertion. Two of the mutations not having been reported in the database so far were novel. Malmo polymorphism (Ala148Thr) was found in two patients. Conclusions: This study confirms the heterogeneity of factor IX gene mutations in northeast hemophilia B patients. The obtained data could be used both in tracking female carriers in families and in making decisions about prenatal diagnosis.