The purpose of this study was to analyze the effects of the pre-treatment method on the measurement of probiotic cell counts. The probiotic cell count was not significantly different in the pre-treatment method such as experimenters, diluted solution, medium, and homogenization duration. The mean value of probiotic cell count with capsule was 2.2×1010±9.5×109 CFU/g. This probiotic cell count was converted into 2.8×1010±1.2×1010 CFU/g based on the net weight. The mean value of probiotic cell count without capsules was 4.3×1010±1.8×1010 CFU/g. As a result of this comparison, probiotic cell count showed significant difference with and without capsules. Thus, it is suggested that the probiotic cell count is measured by removing the capsule in capsule probiotics.