Regulation elements which are normally used in transgenic organisms such as CaMV35S promoter and NOS terminator have potential risk for human health due to their functions. The degradation of non target genes in the RR soybean during the manufacturing process of tofu, soymilk and soybean flour milling, cooking, blending, homogenizing, sterilizing and spray drying was investigated using a sensitive polymerase chain reaction detection system. The system used specific amplification of RR soybean promoter 35S gene and terminator NOS gene. The results showed that the degradation of CaMV35S was more related to its location than to the food processing. The fragment which included soybean genome DNA sequence was more stable than that without soybean genome DNA sequence, but the terminator NOS gene was hardly degraded during each step of the manufacturing process of RR soybean products.