Hemoglobin A1c (HbA1c) is an important parameter for evaluating long-term (6-8 weeks) control of blood glucose levels in patients with diabetes mellitus. We report a Japanese diabetic case who harbored abnormal Hb and demonstrated falsely low HbA1c levels in the regular ion exchange HPLC-based assay. His abnormal β-globin chain had an amino acid replacement that corresponded to glycine to serine substitution at amino acid position 136 of the β-globin chain (Hb Perpignan). Accordingly, a heterozygotic point mutation replacing guanine by adenine at nucleotide position 406 (β136G > S) was identified in the β-globin gene of the proband and his son. These results indicate that the patient had Hb Perpignan, and this abnormal Hb interfered with the HPLC-based HbA1c assay commonly used in the clinic. The cases presented are the first report of patients in the Japanese population harboring Hb Perpignan (β136G > S).