Using genomic DNA prepared from peripheral blood samples of a patient with factor IX deficiency, all eight exons as well as sequences around the splice junctions and putative promoter region of human factor IX DNA have been subjected to polymerase chain reaction (PCR) amplification and sequenced. Comparison of these sequences with normal factor IX gene sequences revealed an insertion in exon VIII that resulted in the alteration of 11 amino acids and the addition of 23 amino acids, all at the carboxy terminal of factor IX. This insertion destroys an Msp I restriction site; carrier detection and antenatal diagnosis in affected kindreds can be performed by testing for the absence of this site. This is the first characterization of a mutation in which insertion in the carboxy terminal region of factor IX causes factor IX deficiency. The genetic change in factor IX in this patient is called Factor IXLincoln Park.