Objectives The influences of Hb variants on HbA1c values can cause mismanagement of diabetes; therefore, the effects of Hb E, H, and G-Taichung variants were evaluated. Designs and methods HbA1c values of 2105 samples, including 37 samples with Hb E, H and G-Taichung variants identified by Hb electrophoresis and the PCR sequence, were evaluated by the ion-exchange (Bio-Rad Variant™ II Turbo analyzer) and boronate affinity (Primus CLC 385 analyzer) high performance liquid chromatography (HPLC) methods. Results In the patients with the Hb E and H variants, their HbA1c values determined by ion-exchange HPLC were significantly higher than those by boronate affinity HPLC. However, there were no significant differences of the HbA1c values in the patients with the Hb G-Taichung variant. Conclusions The HbA1c levels might be interfered by the Hb E and H variants, but not the Hb G-Taichung variant, measured by the Bio-Rad Variant™ II Turbo analyzer.