Background: Heterogeneous mutations in the human coagulation factor IX gene lead to an X-linked recessive bleeding disorder known as hemophilia B. The disease is distributed worldwide with no ethnic or geographical priority.

Materials and Methods: The aim of this study was to characterize the factor IX gene mutations in 28 unrelated Iranian hemophilia B patients. Polymerase chain reaction (PCR) and direct sequencing was performed for all functionally important regions of the gene. Haplotype analysis was performed using three markers.

Results: We identified 24 point mutations and four small deletions (one novel mutation). Overall, 20 different mutations were found and patients with common mutations had identical haplotype.

Conclusion: These data confirm high molecular heterogeneity of the mutations causing hemophilia B and will enable carrier testing and prenatal diagnosis for family members.