Within the frame of our study we investigated Microccocus luteus, Neisseria cinerea, and Pseudomonas fluorescens by means of capillary zone electrophoresis (CZE). They form chains and clusters on a different scale, which can be reflected in the electropherograms. A low buffer concentration of Tris-borate and Na(2)EDTA containing a polymeric matrix of 0.0125% poly(ethylene) oxide (PEO) was used. Key factors were the standardization and optimization of CE conditions, buffer solution, and pretreatment of bacterial samples, which are not transferable to different bacterial strains, in general. The different compositions of the cell wall of on the one hand Gram-positive (M. luteus) and Gram-negative (N. cinerea) cocci and on the other hand Gram-negative, rod-shaped bacteria (P. fluorescens), are probably responsible for the different pretreatment conditions.