Micellar electrokinetic chromatography for the determination of proteins in lactic acid bacterium drink and milk powder is proposed. The effects of several experimental parameters, such as the concentrations of tween-20 and urea in the background electrolyte, ionic strength of the background electrolyte, column temperature and applied voltage, on the separation efficiency of the proteins were studied. Under the optimal conditions, the five proteins in lactic acid bacterium drink and milk powder were separated completely from each other and the discrimination of the lactic acid bacterium drink or milk powder adulterated with soybean proteins was achieved. The present method was applied to the quantitative determination of the milk proteins in lactic acid bacterium drink and milk powder, and qualitative identification of soybean proteins in adulterated samples. The analytical performances of the present method were studied and real samples were analyzed. The relative standard deviations and the recoveries for determining the five milk proteins were satisfactory.