To measure the five classical protein fractions in human serum several electrophoretic techniques are available. Besides separation on cellulose acetate membrane or agarose gel, capillary zone electrophoresis (CZE) may be a useful analytical alternative in clinical routine. We have compared the Dionex CES I capillary electrophoresis system with that of the Olympus Fractoscan using specimens submitted for routine analysis. For clinical evaluation 102 samples from patients with various diseases have been analysed. Serum protein fractions were judged on separation performance, precision and the regression method of Bablok-Passing. Regression analysis revealed variable agreement between both methods with a slope +/- intercept of 2.10-0.52 (alpha(1)-fraction) and 1.0-0.20 (alpha(2)-fraction) as worse and best, resectively; and the coefficient of variation of migration time: 5.9 %-6.8 % (between-run imprecision). Differences in the comparison of fractions are mainly caused by the improved resolution of CZE, e.g. one beta-globulin peak on cellulose acetate is separated into two distinct protein fractions in CZE, including more detailed diagnostic information - as is also the case with gamma-fraction. In some cases monoclonal gammopathy with low concentrations of immunglobulin clone can only be detected in CZE, whereas the cellulose acetate membrane (CAME) electropherogram is inconspicuous. The within-run precision (N = 18) gave coefficients of variation of peak areas 1.3-5.9 % (CZE) and 1.0-3.8 % (cellulose acetate membrane), This is the first time that a complete clinical evaluation of CZE serum protein fraction analysis has been performed, CZE with its higher resolution and hence more detailed diagnostic information in some cases, showed good separation patterns, precision and correlation. Interchangeability of results showed that this CZE method is well suited for analysis of serum protein fractions in clinical routine.