Background: The ALK inhibitor crizotinib offers a new standard of care for patients with EML4-ALK fusion oncogene-positive advanced NSCLC. Two top priorities for its widespread clinical use are to determine: 1) the value of different screening methods for identifying the rare cohort of ALK-positive patients; and 2) the impact of crizotinib on tumor sensitivity to subsequent chemotherapy in ALK-positive tumors. Methods: We previously developed a panel of single and multiplexed RT-PCR assays suitable for rapid and accurate detection of all variants of ALK fusion oncogene transcripts, including all 9 known EML4-ALK fusion gene transcripts and ALK RNA level (Danenberg, ASCO 2010). The sensitivity and specificity on archival formalin-fixed, paraffin-embedded tumor specimens are 99% and 100%, respectively. Results: Between 07/10 and 12/10, 1889 NSCLC specimens in our database were screened for the presence of ALK fusion transcripts. We found 75 (4.0%) NSCLC cases with EML4-ALK fusion positivity, including 38 V1, 7 V2, 4 V3a, 20 V3ab, 4 V3b, and 2 V5a variants. All ALK-positive tumors were adenocarcinomas. Median age (range): 53.3 (33-84). Female/male: 35/40. No EGFR or K-Ras mutation were detected in ALK fusion-positive samples. Further investigation of those samples with high level of ALK expression is ongoing. Expression of chemotherapy-related biomarkers was available from 37 EML4-ALK-positive cases in the database: ERCC1 high/low (13/24), TS high/low/na (13/23/1), and RRM1 high/low/na (18/14/5). The clinical significance of drug target expression remains to be defined in large cohorts of patients with annotated clinical outcomes. Conclusions: Our panel of RT-PCR assays provides a tool for rapid, large-scale screening of NSCLC FFPE tissues for ALK fusion gene transcripts. Head-to-head comparison with other screening methods, such as IHC and FISH, will be required to identify optimal methodology for selection of patients for ALK inhibitor therapy; and will be tested in a developing SWOG trial.