An alpha 1-antitrypsin deficiency associated with pulmonary emphysema was investigated in a 32-year-old Japanese male. Polymerase chain reaction (PCR)-amplified fragments and dot blot hybridization with allele-specific oligonucleotide probes revealed that the patient was homozygous for a C to T transition at codon 53, resulting in the substitution of Phe53 for Ser53 (PI*S(iiyama)). Crossed immunoelectrophoresis after isoelectric focusing and agarose gel electrophoresis showed atypical banding patterns. PI*S(iiyama) is a rare deficiency gene, but it can occur sporadically all over the Japan.