We identified a structural defect of alpha-galactosidase A (alpha-Gal A) gene in a Japanese patient with Fabry disease. A partial deletion approximately 0.4 kilobase-pairs in size was delineated by restriction endonuclease mapping; whole exon 3 sequence was removed. alpha-Gal A mRNA was deficient in the mRNA preparation from the lymphoblastoid cells derived from the patient, and a faulty transcription resulting in an unstable alpha-Gal A message was suggested in this case. Molecular pedigree analysis was successfully performed in identifying heterozygotes and the ancestry of the mutant allele in this family.