ObjectiveTo detect the frequency of anaplastic lymphoma kinase (ALK), ROS1 and RET fusion genes in non-small cell lung cancer (NSCLC) patients in Sichuan, and analyze their correlation with clinical features of NSCLC. MethodsReverse transcription-polymerase chain reaction (RT-PCR) was performed to examine gene rearrangement of ALK, ROS1 and RET fusion genes in 310 NSCLC patients who were admitted in Department of Pulmonary Neoplasm of Sichuan Cancer Hospital from March 2009 to March 2012. There were 234 male and 76 female patients with their median age of 60 years (range, 29 to 77 years). There were 164 patients with a smoking history. Histological types included adeno-carcinoma (AC) in 142 patients, squamous cell carcinoma (SCC) in 138 patients, adenosquamous carcinoma in 10 patients, and other types in 20 patients. Patients, gender, age, smoking history, histological types and TNM staging were also collected. Correlations between fusion genes and clinical features were analyzed. ResultsAmong the 310 patient:15 patients with ALK fusion genes were identified (EML4-ALK) with a positive rate of 4.84%, including 14 patients with AC and 1 patient with SCC. ALK fusion genes were more common in patients under 60 years, without a smoking history, and with AC (P < 0.05). ALK fusion genes were not significantly correlated with gender or histodifferentiation. One patient with ROS1 fusion genes (CD74-ROS1) was identified with a positive rate of 0.32%, who was AC patients. Two patients with RET fusion genes (KIF5B-RET) were identified with a positive rate of 0.64%, both of whom were AC patients. ConclusionsGene rearran-gement rates of ALK, ROS1 and RET in NSCLC patients in Sichuan are 4.84%, 0.32% and 0.64% respectively. Patients with negative gene mutation of epithelial growth factor receptor (EGFR), AC, younger age, without a smoking history or with a light smoking history are more common to have ALK gene rearrangement. Gene rearrangement rates of ROS1 and RET are low, and their clinical significance needs more research.