Genetically modified (GM) crops are widely cultivated in many countries and the number of commercially available GM events has been rapidly increasing. This situation necessitates efficient analytical methods for ensuring the compliance with regulations relevant to GM organisms (GMOs). We developed a real-time PCR array method as an analytical platform for comprehensive GMO detection. Primer-probe sets for the specific detection of GM events, recombinant DNA segments, taxon-specific endogenous genes and so on were designed, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The DNA extract from an analytical sample was mixed with a real-time PCR master mix and placed in the wells of the plate. Finally, the positive/negative results were determined from the obtained amplification curve for each well. Analytical performance, such as specificity and sensitivity, were evaluated in house and then the method was validated. Furthermore, a comparative analysis of the test result and publicly available information on GM crops approved in Japan allowed us to potentially identify unapproved GM crop contamination.