We have identified an MseI restriction fragment length polymorphism (RFLP) in the 5' flanking region of the factor IX gene. RFLPs in the factor IX locus are routinely used as linkage markers to track defective factor IX genes through affected pedigrees, allowing diagnosis of the haemophilia B carrier state in female members of the kindred. Currently, seven intragenic polymorphic loci have been characterized allowing carrier diagnosis in 89% of cases in the Caucasian population. Additional screening with the MseI RFLP reported in this publication increases this figure to 94% of cases. In Asian populations only one of these RFLPs (HhaI) is present at any significant frequency. Hence, carrier detection rates are much reduced in comparison to the corresponding figure of 89% in Caucasians. We report that this MseI RFLP is also present in the Thai population. Indeed, when used in combination with the HhaI polymorphism, the MseI RFLP should significantly improve the carrier detection rate in the Thai population from 11% to 40% of cases.