R-phycoerythrin (PHYCO, M-r 240 000), glucose-6-phosphate dehydrogenase (GPD, M-r 104 000) and two charge isomers of recombinant green fluorescent protein (GFP-1 and GFP-2, M-r 27 000) were subjected to capillary zone electrophoresis (CZE) In capillaries of 50, 100 and 150 mu m inner diameter at various sample concentrations, electric field strengths, and lengths of the initial zone with the purpose of testing the hypothesis that protein - capillary wall interactions rather than thermal effects are predominantly responsible for the peak spreading of proteins in CZE. The efficiency of CZE was expressed in terms of the number of theoretical plates, N, or the plate height corrected by subtracting the contribution from initial zone length, H'. The latter has the advantage of solely reflecting contributions to the separation efficiency arising from intracolumn peak spreading in capillaries of different diameters. The separation efficiency measured varied widely, by two orders of magnitude, for these proteins under identical conditions, with GPD exhibiting the highest and PHYCO the lowest values of N. H' was found to be independent of sample concentrations within the concentration ranges studied, 1-100 mu g/mL for PHYCO and 100-1000 mu g/mL for GPD, while exhibiting a decrease with sample concentration for GFP, especially in 150 mu m diameter capillaries, within the concentration range 1-100 mu g/mL. H' was also found to be independent of electric field strength up to 300-400 V/cm for PHYCO and GFP. In all experiments, the CZE of proteins in 100 mu m diameter capillaries provided a higher or, at least, equal efficiency, compared to that in 50 or 150 mu m diameter capillaries. It may be concluded that the protein - capillary wall interactions and protein microheterogeneity are the dominant sources of peak spreading and their specific combinations are thought to be responsible for the wide variation in separation efficiency between proteins in CZE observed under identical conditions.