Direct analysis of microbes such as either gram-positive or gram-negative bacteria without cell lysis was investigated using capillary electrophoresis. Bacteria cells were directly introduced into the microbore fusedsilica capillary, then separated under high electric field in less than 15 min. It was found that a proper dispersion of bacteria cells was important for reproducible results. Migration behavior of bacteria at different storage condition was investigated and many unexpected peaks were observed from bacteria stored at room temperature due to the distortion of cells. This phenomenon was attributed to the change of size and shape of the same bacterium and confirmed by the scanning electron microscopic images.