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We evaluated the analytical performances of the new Sebia kit for quantification of hemoglobin fractions (HbA, HbF and HbA2) and structural hemoglobin variants on the Capillarys® system. This automated capillary zone electrophoresis method uses an alkaline buffer with silica capillaries and spectrophotometric detection. Specimen stability was evaluated during 1 month. The reproducibility of migration and the imprecision of quantification were also investigated. Comparison with the Beckman P/ACE® system was performed on 202 samples. A total of 131 subjects without any hematological abnormality were analyzed to establish the HbA2 reference ranges based on our local population. Quantification of the Hb fractions and variants exhibited excellent stability for 4 weeks of storage at 4°C, with CVs >0.3%. The imprecision of the migration normalized to that of HbA2 for all hemoglobins tested (fractions and variants) was low, with a CV of −2.5%. At physiological and pathological levels, total imprecision ranged from 1.9% to 4.6% for HbA2, from 0.6% to 9.7% for HbF, and from 0.6% to 1% for HbS. Statistical analysis revealed a small proportional negative bias for HbA2 (−8.6%). Small systematic bias (−0.2%) and proportional bias (−28%) were observed for HbF. No statistically significant difference was found for HbS. The reference range for HbA2 was 2.1–3.2%. The Capillarys® system is a fully automated and accurate system that gives high-resolution performance and displays appropriate characteristics for use as a routine method for the diagnosis of thalassemias and hemoglobinopathies.