Background: We conduct the nationwide cancer genome screening project in Japan since 2015 using Next Generation Sequencing in advanced non-colorectal gastrointestinal (GI) cancer (aNon-CRC), called as SCRUM-Japan GI-SCREEN 2015-01-Non CRC. The objective is to evaluate the frequency of cancer genome alterations in aNon-CRC and to identify patients (pts) who are candidate for clinical trial for corresponding targeting agents. Methods: Pts with aNon-CRC including esophageal cancer (EC), gastric cancer (GC), and other types of aNon-CRC. Twenty ng of DNA and 10 ng of RNA were extracted from FFPE tumor samples and were analyzed by the Oncomine Cancer Research Panel (OCP) which allows to detect gene mutation, copy number variant (CNV) and fusions across 143 genes in a CLIA certified CAP accredited laboratory. The detected genomic variant data were classified according to whether genetic driver of cancer including gain- and loss-of-function or single nucleotide variant based on the Oncomine Knowledgebase. Results: As of October 31^st in 2015, a total of 243 GC and 85 EC pts were enrolled and 235 GC and 83 EC samples were available. A total of 231 GC and 79 EC samples were analyzed and four GC and EC samples each are currently under analysis. The sequence with the OCP was successfully performed in 174 GC (75.3%) and 52 EC (65.8%). The most frequently detected mutations were TP53 (48.3%), PIK3CA (6.9%), KRAS, and SMAD4 (5.7%) in GC and were TP53 (76.9%), NFE2L2 (25.0%), CDKN2A, and PIK3CA (9.6%) in EC. Those of CNVs were ERBB2 (8.6%), CCNE1 (5.2%), FGFR2, and KRAS (4.0%) in GC and were CCND1 (44.2%), EGFR (13.5%), and SOX2 (9.6%) in EC. WIPF2-ERBB2 fusion and EGFR vIII were detected in GC and FGFR3-TACC3 fusion was detected in EC. Pts with PIK3CA or AKT1 mutation, MET or FGFR2 amplification and FGFR3-TACC3 fusion were enrolled in early clinical trials. Conclusions: This nationwide screening system is efficient to detect rare mutations in GI cancer. This novel knowledge provides an intriguing background to investigate new target approaches and represents a progress toward more precision medicine. Clinical trial information: UMIN000016344.