Japanese bacillus Calmette-Guerin (BCG) vaccine preparation contains two types of variant strains, Type I, which has a 22-base-pair deletion in the RD16 region, and Type II, which has an identical sequence to those of other BCG strains. In this study, we established a method to quantify the percentage of variant strain Type II contained in freeze-dried BCG product with real-time PCR. With this method we examined the master seed lot Tokyo 172, two secondary seed lots, Tokyo 172-1 and Tokyo 172-2, which were produced from Tokyo 172, and four commercial lots produced form Tokyo 172-1. Tokyo 172, Tokyo 172-1, and Tokyo 172-2 contained 55.1%, 19.5%, and 3.6% of Type II variant strain, respectively. Commercial lots contained 1.5%, 4.5%, 7.4%, and 4.3% of Type II variant strain, respectively. These results indicated that the two variant strains contained in the master seed lot continued to coexist in subsequently produced lots with a decrease in population of variant strain Type II. This method would be useful for quality control of commercial Japanese BCG vaccine preparations.