Qualitative and real-time quantitative PCR methods were developed to facilitate the investigation of the persistence of hpt gene within transgenic rice in different processed foods and degradation test in vitro and in vivo. Using rbcl gene fragment as inner positive control, a fragment-multiplex PCR system was established to detect fragments of the hpt gene of genetically modified rice with lengths between 236 bp and 910 bp, the amplified fragment was further confirmed via DNA sequencing. The 236 bp minimal fragment of qualitative PCR were cloned in the vector pUC18-pMD T and used as external standards of quantitative PCR. The real-time quantitative PCR method was developed based on TaqMan technology by the MGB probe for detecting the inserted DNA, which showed a good linear correlation (R~2=0.998) and precision at wide range between 10 and 10~5 DNA copies per reaction, and detection limit was 10 copies. The results indicated that the quantitative PCR system could work reliably and stably and fit well with the aim for monitoring degradation of hpt gene in different processed food and degradation process in vitro and in vivo.