Background: Various driver gene alterations have emerged as critical targets for molecular therapies in non-small cell lung cancer (NSCLC), but these alterations other than EGFR mutations occur in rare populations. A nationwide genomic screening network in Japan (LC-SCRUM-Japan) was established in February 2013 for the development of novel targeted therapies against advanced NSCLCs harboring these rare alterations. Methods: Advanced non-squamous NSCLCs without EGFR mutations were eligible for inclusion in LC-SCRUM-Japan. The tumors were analyzed for ALK/RET/ROS1 fusions using RT-PCR, and detected fusions were confirmed by FISH. Between November 2013 and March 2014, fusion-negative tumors were further examined for other driver gene mutations using a next-generation sequencing (NGS) system (Ion PGM with Ion Torrent AmpliSeq Cancer Hotspot Panel, version 2), enabling the simultaneous analysis of 50 cancer-related genes. Results: As of December 26, 2014, a total of 188 institutions across Japan were participating and 1347 patients had been enrolled in LC-SCRUM-Japan. Among 1271 available samples, ALK/RET/ROS1 fusions were detected in 24 (2%)/31 (3%)/55 (4%) cases, respectively. The NGS analysis was performed in 201 cases without the fusions, and 82 cases (41%) had driver mutations, including 45 KRAS mutations (22%), 10 BRAF mutations (5%), 9 ERBB2 mutations (4%), 2 PIK3CA mutations (1%), and 1 NRAS mutation (0.5%). MET and ERBB2 amplifications were also detected by the NGS in 4 (2%) and 2 (1%) cases, respectively. Among a total of 198 cases harboring targetable gene alterations, 16 with RET fusions, 26 with ROS1 fusions, and 2 with BRAF mutations were enrolled in clinical trials for vandetanib (LURET study, Japan), crizotinib (OO12-01, East Asia), and dabrafenib (BRF113928), respectively. Conclusions: This nationwide and population enrichment screening system enabled various rare driver gene alterations to be efficiently detected in advanced NSCLC, thereby contributing to the rapid accrual of matched patients in clinical trials for targeted therapies.