Fusion oncogene has been identified as one of driver mutations in NSCLC. We searched for EML4-ALK and CCDC6-RET fusion genes in NSCLC and analyzed their relationship with clinicopathologic features. Fusion oncogenes EML4-ALK and CCDC6-RET were identified by reverse transcriptase-polymerase chain reaction (RT-PCR) in 156 surgically resected NSCLCs - 52 squamous cell carcinomas (SCCs) and 104 adenocarcinomas (ACs). In addition, mutations of EGFR, ERBB2, KRAS, NRAS, BRAF, PIK3CA, PTEN, and LKB1 were determined by PCR and direct sequencing. The EML4-ALK was found in 4 (2.6%) of 156 NSCLCs; 3 (2.8%) of 107 ACs. For EML4-ALK, all four cases were detected in younger patients (≤ 64 years old), three in males, three in ever smokers. The CCDC6-RET were found in 4 (2.6%) of 156 NSCLCs; 4 (3.8%) of 107 ACs. For CCDC6-RET, all four cases were found in never-smoker ACs, two in younger patients, and two in females. One of the four EML4-ALK positive cases also had a KRAS mutation. However, none of four CCDC6-RET positive cases harbored any other mutation. Overall, among the 156 NSCLCs, a total of 55 genetic alterations were detected in 51 (32.7%) tumors - 7 (14.3%) in SCCs and 44 (41.1%) in ACs. Genetic alterations were significantly more frequent in women, never smokers and ACs than in men, ever smokers and SCCs (p=0.001, p=0.003 and p=0.001, respectively). The mutations occurred in a mutually exclusive pattern. Here we report the frequency of EML4-ALK and CCDC6-RET fusion oncogenes in Korean NSCLC.