We have used the polymerase chain reaction (PCR) to amplify specific DNA fragments of the Mycobacterium bovis BCG (BCG) vaccine from genomic DNA. We have used capillary electrophoresis (CE) to analyze and detect the PCR products. The ability to amplify a DNA fragment of about 350 bp will bring the speed and simplicity of PCR to vaccine identification in a genomic DNA, and even to quantitative DNA research. While current methods for determining the identity of BCG vaccine are very labor intensive, in this paper we will describe a PCR and CE technique for identifying the BCG vaccine. Thus, the identification of PCR products by CE may offer better resolving power, convenience, and quantitative capability than the conventional electrophoresis methods.