We studied whether problems quantifying hemoglobin A(2) (HbA(2)) could be resolved by using capillary electrophoresis. HbA(2) was quantified on whole blood samples from patients with and without beta-thalassemia trait and patients heterozygous for HbE, HbS, HbC, and HbD Punjab using the VARIANT II beta-thalassemia (Bio-Rad, Hercules, CA) and Capillarys 2 (Sebia, Norcross, GA). HbA(2) results in patients with and without beta-thalassemia trait were lower with the Capillarys 2 system. Reasonable HbA(2) results were obtained for patients with HbD Punjab and HbE traits on the Capillarys 2. HbA(2) results for patients with HbS, heterozygous and homozygous, were similar by both methods. Interference due to coelution for HbA(2) results for patients with HbC trait was noted on the Capillarys 2. Between-day imprecision on the VARIANT II is less than that for the Capillarys 2 system. The Capillarys 2 is superior to the VARIANT II for quantifying HbA(2) in the presence of HbE and HbD Punjab traits. The Capillarys 2 offers only slight advantages over the VARIANT II for quantifying HbA(2) in the presence of heterozygous and homozygous HbS. The Capillarys 2 gives inferior HbA(2) results for patients with HbC trait.