Hemophilia B (HB) is an X-linked recessively inherited bleeding disorder caused by heterogeneous mutations in the factor IX gene.We screened for mutations in HB patients using a combination of multiplex polymerase chain reaction, conformation sensitive gel electrophoresis, and DNA sequencing. Phenotypic analysis was performed using 1 stage assay for factor IX: C activity and enzyme-linked immunosorbent assay for factor IX: Ag. Haplotype analysis was performed using the common polymorphic markers of the factor IX gene.Seventeen novel mutations comprising of missense mutations, nonsense mutations, and small deletions were detected. Haplotype analysis indicated that some of the patients had a common haplotype background but had different molecular defects thereby suggesting that all the mutations arose de novo. Phenotypic data suggested that about one-fourth of the patients (23%) had antigen-activity discordance. Furthermore, it was observed that a majority of the molecular defects (71%) were located in exon H of the factor IX gene. The mutation screening strategy was thus modified wherein exon H was screened first followed by screening of other exons.The present findings suggest that there is a wide phenotypic and genotypic heterogeneity in HB. Presence of more than 70% of mutations in exon H of the factor IX gene allows us to adopt a cost effective screening strategy in offering genetic diagnosis to the affected families.