The aim of this study was to develop a method for simultaneous detection of a variety of genetically modified (GM) rice ingredients in foods using multiplex polymerase chain reaction (PCR) coupled with high-performance liquid chromatography (HPLC) assay. The following exogenous genes found in GM rice were selected as targets: CaMV35S, NOS, Cry1Ac, Bar, and Xa21. The endogenous gene PEPCex of rice was selected as an internal control. In brief, six pairs of primers for multiplex PCR were designed according to the specific region of CaMV35S, NOS, Cry1Ac, Bar, Xa21, and PEPCex, and following the optimization, a multiplex PCR assay was developed, and then the multiplex PCR products were subjected to HPLC analysis. The GM rice lines ShanYou 63, KeFeng 6, KangYou 97, and LLrice 62 were used as reference GM rice samples to evaluate the potential diagnostic capability of the method. Results demonstrated that the multiplex PCR-HPLC developed in this work was an efficient diagnostic method for simultaneous identification of the target genes with 0.15 ng/mL of high sensitivity, suggesting a better alternative for the rapid detection of many genetic modification events.