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Introduction Denaturing High Performance Liquid Chromatography (DHPLC) is accurate, sensitive, economic and high-throughput for detecting mutation.We aim to establish a feasible protocol to provide genetic diagnosis and prenatal diagnosis for Chinese hemophilia B patients and carriers by DHPLC and direct-sequencing.Methods The genetic diagnosis was performed on 5 unrelated families, and 4 of them asked for prenatal diagnosis.Results The results of DHPLC and Sequence analysis indicated that the patients and carriers from five families have the pathogenic mutations,c.1022G>A(p.R341Q),c.484C>T(p.R 162X),c.1135 C>T(p.R3 79X),c.799C>T(p .H267Y) and c.1232G>T(p.S411I), respectively.Except c.484C>T(p.R162X), the other 4 mutations were firstly reported firstly in Chinese population.During prenatal diagnosis, one of the fetuses was found to be hemizygote with the c.484C>T(p.R162X) mutation and another two fetus were found to be carriers of c.484C>T/C(p.R162X/C) and c.799C>T/C(p.H267Y/H) respectively.The remaining two fetuses were diagnosed as normal and it was verified after they were born.Conclusion A combination of DNA direct-sequencing with DHPLC is rapid and accurate for the genetic diagnosis including prenatal diagnosis of hemophilia B disease.Additionally, the level of F9 clotting activity in umbilical cord blood couldnt be used as a reference resource in the prenatal diagnosis of HB.