Seven hemophilia B patients with anti-factor IX antibodies are studied with molecular means. A total factor IX gene deletion was detected in four patients from three distinct families. Three other patients without detectable gene arrangements were investigated at the DNA sequence level. Enzymatic amplification of the factor IX gene and subsequent DNA sequencing revealed four novel nucleotide mutations in these patients. Patient HB 5 had two point mutations in his factor IX gene. One is located at nucleotide -793 from the translation start (G-A) and the other (C-T) was found in the codon for 191-Gln changing to a termination codon. Patient HB6 had a point mutation (G-A) in the splicing junction of intron g. A2 bp nucleotide deletion was detected in the third exon of the patient HB7 yielding 8 frameshifted amino acids and a stop codon. These results suggested that not only a large deletion of the factor IX gene but also point mutations or small deletion of the gene which may cause the substantial loss of the coding information for the mature protein are involved in the development of anti-factor IX antibodies in hemophilia B patients.