Nucleotide-based amplification method is an important system for the identification of genomic modified foods (GMF). Roundup Ready Soybeans (Monsanto company), Bt 176 GM maize (Novartis/Ciba-Geigy company) and Cecropin D capsicum was used as material to search for the feasibility of investigating the safety of GMF by PCR method. Primers specific for inserted genes and crop endogenous genes in Roundup Ready Soybeans, Bt 176 maize and Cecropin D capsicum were applied. The discrimination system for GM soybeans, GM maize and GM capsicum from the counterpart of non-GM products and the detection system for correlating marker genes and transgenes are established. The method was easy and fast, and the corresponding results fixed the standard or declared data.