We have investigated genomic DNA samples of 24 patients with hemophilia B (factor IX deficiency), including seven patients with anti-factor IX antibodies (inhibitors), by molecular probes. Seventeen patients without inhibitors against factor IX and three patients with inhibitor showed no abnormalities in their restriction fragments generated by digestions of the genomic DNA by BamHl, EcoRl, Mspl, or Taql and hybridized with a factor IX cDNA probe (pHFIX). The remaining four patients with inhibitors were found to have gross deletions of the factor IX gene. Among those four patients, two were from the same family. Quantitative Southern blotting clearly showed that the abnormal gene was inherited in this family. DNA from the mother of another patient with deletion of the factor IX gene showed normal gene dosage, indicating that the mutation must have occurred at the mother's germ cells. The genomic DNA samples of four patients with gross factor IX gene deletions were found to lack the entire factor IX gene as analyzed with a factor IX cDNA as well as with a 3'-genomic factor IX fragment as probes. The hypoxanthine phosphoribosyltransferase (HPRT) gene probe, however, was found to hybridize with all of these DNA samples, indicating that the deletions in these genomic DNA samples had not extended to the region containing the HPRT gene locus in q27 proximal to the factor IX gene locus on the X chromosome. Several clinical characteristics were compared between inhibitor cases with gene deletion and inhibitor cases without obvious gene deletion.(ABSTRACT TRUNCATED AT 250 WORDS)