The varieties of commercially available genetically modified (GM) crops are rapidly increasing, and this situation demands analytical methods capable of detecting recently developed GM crops. Here we review our research activities to develop and validate new analytical methods for recently distributed GM crops. For the screening analysis of GM content in analytical samples, we developed real-time PCR-based quantitative methods for two GM maize events, MIR604 and MIR162. To accurately analyze GM content irrespective of the commingling of stacked GM events, we developed the group testing method. For the comprehensive analysis of various GM events, the real-time PCR array method was established. In November 2016, the Consumer Affairs Agency of Japan released the standard testing manual including these new testing methods to ensure the validity of the food labeling system in Japan. Given the expected increase in the number of GM events to be analyzed in the future, we need to keep working toward the realization of simple and comprehensive detection and quantification methods that can be used for the increasing number of these events.