In this report we summarize evaluation data of an automated capillary zone electrophoresis (Capillarys II, Sebia, France) in comparison to a conventional cellulose acetate electrophoresis system (Hite320, Olympus, Germany). Serum samples from 428 blood donors were analysed to evaluate gender-specific reference intervals, which revealed significant percentage differences between male and female. In contrast to conventional electrophoresis methods all lipoproteins co-migrate with the albumin fraction using capillary electrophoresis. Comparisons between both separation methods and quantitative determinations of albumin/total protein show a better correlation between the albumin fraction determined by capillary electrophoresis and the quantitative determinations. A transversal evaluation of serum protein fractions should be performed within one day due to the combination of effects based on serum sample instability and method imprecision.