In this study, we used polymerase chain reaction (PCR) to detect genetically modified Roundup Ready soybean (RRS) in miso. Several different DNA extraction methods had been tested. The CTAB method published by Lipp et al. and a commercial kit,Nucleospin Food, were used, because they had the most appropriate performance for miso sample. Four pairs of primers specific for the inserted genes and crop endogenous genes in RRS were applied in PCR. Using these primers, the method showed a false-negative result for the miso sample during a later period. When another more sensitive method, nested-PCR had been used, we obtained false-negative result for the sample in later fermentative stage. Since PCR and nested PCR can not yield to positive results, using these two methods to detect transgenic components in miso is not efficient.