Background: Chromosomal rearrangements resulting in expression of oncogenic receptor tyrosine kinase fusions occur in a subset of epithelial malignancies and can underlie sensitivity to tyrosine kinase inhibitors. In non-small cell lung cancer (NSCLC), rearrangements involving anaplastic lymphoid kinase (ALK), ROS proto-oncogene 1 (ROS1), and RET proto-oncogene (RET) occur at frequencies of approximately 4%, 1% and 1%, respectively. Rearrangements involving neurotrophic tyrosine kinase receptor type 1 (NTRK1) have been described, though the frequency is not well characterized. Methods: We implemented a multiplex polymerase chain reaction (PCR) technology, Anchored Multiplex PCR (AMP), for detection of fusion transcripts using targeted next-generation sequencing of cDNA generated from clinical samples (Zheng et al., 2014). The sequencing library targets known fusion exons in ALK, ROS1, RET and NTRK1. We retrospectively reviewed the NSCLC cases assessed by this method. Results: Between July 2013 and January 2015, 663 clinical NSCLC cases from our institution were assessed, providing > 99% power to detect at least one fusion event at an underlying frequency as low as 1%. 584 cases were adenocarcinoma histology. We detected fusions involving ALK, ROS1, RET and NTRK1 at frequencies of 2.6%, 0.9%, 2.0% and 0.0% (17, 6, 13 and 0 cases), respectively. All were mutually exclusive. The histologic subtype was adenocarcinoma in all fusion cases except one. The average age at diagnosis was 57.0, 55.9 and 58.3 years, and average pack years were 8.5, 5.8 and 7.7 for patients with ALK, ROS1 and RET fusions, respectively. The ALK fusion partner in all cases was EML4; ROS1 fusion partners were SDC4, CD74, and EZR; and RET fusion partners were KIF5B, CCDC6, RUFY2 and TRIM24. Although no NTRK1 fusion was detected in NSCLC, we detected a PPL-NTRK1 fusion in a thyroid carcinoma. Conclusions: With this method, we identified ALK, ROS1 and RET fusions at frequencies and with patient characteristics consistent with previous studies. NTRK1 fusions appear to be rare in NSCLC, though it is possible that this assay may not detect all fusions.