identification of microbial contamination by CE has interested many researchers mainly because of the high speed of CE analysis. However, the CE separation of such big structures brings a lot of questions mainly about the behavior of microorganisms and about the mechanism of separation. In this work, we constructed a simple apparatus where a microscope was used as one detector and a UV detector was used as the second one and we made the comparison of three typical setups for CE of microorganisms. Saccharomyces cerevisiae was chosen as a model microorganism and was analyzed in bare fused-silica capillaries, covalently modified capillaries and dynamically modified capillaries by poly(ethylene oxide) or CTAB. Results showed that the use of CE instrument directly connected with a microscope could be advantageous for the study of separation mechanisms and/or migration behavior.