Abstract Background National guidelines advocate broad molecular profiling as part of the standard diagnostic evaluation for advanced non-small cell lung cancer (NSCLC), with the goal of identifying driver mutations for which effective therapies or clinical trials are available. However, adherence to genomic testing guidelines may present challenges to community oncologists. Methods Retrospective review of genomic testing patterns in patients with non-squamous NSCLC treated by 89 oncologists at 15 sites throughout New Jersey and Maryland between January 2013 and December 2015. Results 814 patients (89% stage IV; 11% stage IIIB) were identified in the COTA database. 479 (59%) met guideline recommendations for EGFR and ALK biomarker testing; 63 (8%) underwent comprehensive genomic profiling (CGP) for all four major types of alterations (point mutations, indels, fusions and copy number amplifications). Gender, age, race, site of care (referral vs. community center), and practice size did not influence CGP frequency. Active smokers and patients who died within 30 days were tested less frequently (p<0.05). Among those not tested for EGFR and ALK , 52% received chemotherapy without documented reasons for non-testing, 32% did not receive anti-neoplastic therapy and 13% had insufficient tissue for genotyping. Conclusions Genomic testing presents multiple logistical challenges for the community based oncologist, including coordination of sample handling, long turnaround times, test reimbursement, access to targeted therapies, insufficient tissue, and the patient harm from repeat biopsies necessary if tissue is insufficient. Opportunities exist for improvement in guideline adherence, possibly through new technologies such as “liquid biopsies,” which obviate tissue biopsy in select settings.