Measurement of organic acids derived from metabolites of biologically nourishing species of bacteria in fermented soybean milk was studied in this paper. In gas-liquid chromatograpth it is very necessary to pretreat the sample due to its high content in proteins and nonvolatile solubles. Firstly, for the pretreatment the precipitation of proteins in fermented soybean milk with diatomites was carried out. Moreover, as short-chain fatty acids and their esters are highly volatile and water soluble, it is rather difficult for measurement by gas-liquid chromatograpty. Therefore, a method of benzyl esterification was adapted in the experiment. The experimental results showed high precision and good recovery. In addition, organic acids in some tonic oral liquids and yogurts were also measured.