This study compares two automated capillary electrophoresis (CE) systems, the Capillarys 2 (Sebia, Surrey, UK) and V8 (Helena Biosciences, Tyne and Wear, UK) for the measurement of carbohydrate-deficient transferrin (CDT). Analytical imprecision was calculated for both platforms using internal quality control material from Sebia and Helena Biosciences, while a patient comparison was performed on 150 patient samples with CDT% levels ranging from 0.3% to 23.7%. Inter- and intra-assay imprecision between the two platforms were comparable. The correlation between platforms using patient samples was r2 = 0.985. However, there was a significant proportional bias at higher CDT concentration ranges, with the Helena system showing negative bias but good correlation over the clinically significant range. Analytical performances from both CE systems have been proven as suitable for routine laboratory use. The V8 CDT results were comparable to the Capillarys 2 in human sera over the clinical range of interest.