Hemophilia B is rare in females and only a few cases have been reported. In this report, we describe a girl with a clinically severe course of hemophilia B but with a normal 46,XX karyotype. She had no signs of Turner’s syndrome or any other dysmorphic features. She was demonstrated to have moderately decreased factor IX levels (factor IX:C, 1.5 units/dl; factor IX:Ag, 2.2 units/dl). Her father and paternal uncle were also found to be deficient in factor IX and her mother seemed to carry a factor IX gene mutation with intermediate factor IX:C and factor IX:Ag levels (factor IX:C, 46 units/dl; factor IX:Ag, 39 units/dl). The maternal grandmother also showed mildly decreased factor IX:C and factor IX:Ag levels (factor IX:C 41 units/dl; factor IX:Ag 32 units/dl), further confirming the mother’s carrier status, which was indirectly confirmed by DNA segregation analysis using the polymorphic markers of the factor IX gene, as none of her other family members were found to be deficient in factor IX. However, the <i>Dde</i>I polymorphic marker of the factor IX gene for which the mother was informative showed the inheritance of a ‘369-bp’ allele in the mother, which was different from the ‘319-bp’ allele found in all of her 3 brothers who had normal levels of factor IX. Intermediate levels of factor IX in the mother and the maternal grandmother, severe deficiency of factor IX in the child and the polymorphic allele different from that of the normal subjects in the family are all consistent with a homozygous or double-heterozygous condition in this child.