Analysis of health-related microbes called probiotics was performed by capillary electrophoresis. A rapid and easy characterization for two important probiotics, Saccharomyces cerevisiae and Enterococcus feacalis, was obtained in the running buffer containing poly(ethylene oxide). Quantitation of probiotic (Saccharomyces cerevisiae) shows a good linearity between the peak area versus the concentration of microbe. From the comparison of electropherograms of antidiarrhea, it was found that capillary electrophoresis could be employed for the quality control and quality assurance for the production of a medicine containing the probiotics.