Hemoglobinopathies are genetic disorders of globin chains characterized by the decreased expression of α- or β-globin chains (thalassemias) or by the synthesis of an abnormal protein (hemoglobin variants in, e.g., sickle cell disease). The screening of most hemoglobinopathies relies, together with hematological results and clinical elements, on the separation and quantification of normal and abnormal hemoglobin fractions. Gel electrophoresis, isoelectric focusing, and HPLC have been the methods of choice for many years. For about 20 years, capillary electrophoresis has appeared as a strong alternative method. Since the early 2000s, automated instruments are commercially available for the analysis of Hb fractions in adult patients but also for neonatal screening.