Clinical laboratory evaluation of congenital hemoglobin disorders requires both the accurate identification of major and minor hemoglobin variants, and precise quantitation of these variants over a wide range of concentrations. Capillary isoelectric focusing is an automated, microanalytical technique that produces diagnostic information comparable to that obtained from multiple conventional assays now used by most hospital laboratories. This report describes the advantages of capillary isoelectric focusing for the routine primary assessment of hemoglobinopathies and thalassemias. The use of capillary isoelectric focusing for the identification of unusual hemoglobinopathies, including an extremely rare doubly heterozygous disorder (hemoglobin C/E disease), is described. Application of the technique for rapid (< 4 minutes) neonatal hemoglobinopathy screening, and for the analysis of Hb A1c to monitor glycemic control in diabetic subjects is also discussed. In an increasingly competitive and cost-conscious clinical diagnostic market, capillary isoelectric focusing is a rapid, specific, precise, and low-cost method for comprehensive primary analysis of hemoglobin variants.