A new Taq I polymorphism in Alu repeat 4 of the human factor IX gene i
s reported. This polymorphism is associated with a C-T transition at t
he 72-bp position of the Alu repeat consensus sequence. A simple PCR s
ystem for testing of this structural anomaly, with internal control of
restriction hydrolysis, was developed. The frequency of the new polym
orphic site and its linkage with other polymorphisms of the factor IX
gene were also evaluated. The new polymorphism was used for establishi
ng hemophilia B carriers.