Tofu samples, which were purchased in the Tokyo and Kanagawa markets before and after the enforcement of the mandatory labeling system (April 1, 2001) for genetically modified (GM) foods, were examined by qualitative PCR to detect the recombinant DNA of the Roundup Ready soybean. The recombinant DNA was detected in 13 of 30 tofu samples purchased before the enforcement. Of those with detected DNA, eight samples were labeled as "non-GM". For the samples purchased after the enforcement, the recombinant DNA was detected in 7 of 25 tofu samples and all of the positive ones were labeled as "non-GM". The GM soybean contents of the material soybean for the tofu samples showing positive recombinant DNA and labeled as "non-GM" were estimated by quantitative PCR using the ABI 7700 system. The results suggested that all of the tofu samples were made from soybean containing less than 1% of the GM one. In the mandatory labeling system, agricultural products can be regarded as non-GM when it is confirmed that they are treated under the "Identity Preserved (IP) Handling" during their production/distribution processes and it is well recognized that unintentional mixing is inevitable even during the IP handling of products. Therefore, we concluded that the non-GM labeled tofu samples showing positive recombinant DNA were made from IP handling soybeans, based on their low GM soybean contents.