Indirect genetic diagnosis using polymorphic DNA markers can be useful in large-scale screening programs, which is technically simpler, more rapid and amenable. The main objective of this study was to test the informativeness of two common intragenic markers (TaqI and XmnI) in Iranian haemophilia B families to detect the carriers by using a strategy that would be accurate and informative, yet less expensive compared to direct mutation analysis. The efficacy of these sites has been examined in 50 unrelated Iranian haemophilia B families and 50 normal females. The method used was polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP), which is economical and the enzymes XmnI and TaqI are cheap enough to be accessible in most of laboratories in developing countries. Our results show that 25% of X-chromosomes had the restriction site for TaqI enzyme. The XmnI site was 21%. The heterozygosity rates for TaqI and XmnI polymorphisms were 37% and 38%, respectively. Using the two polymorphisms together, the informative rate reached 46%. Taking advantage of TaqI and XmnI polymorphisms, carrier detection was performed for seven females with unknown status in five haemophilia B families (including one large extended family) with positive history. Six of the girls were normal and one was haemophilia B carrier. Therefore, carrier detection might be possible for informative Iranian haemophilia B families in the familial cases. Additionally, similarities in term of heterozygosity rates for these two polymorphic sites were seen between some European and Iranian populations.