Recent advances in therapy for non-small cell lung carcinoma have shown that a personalized approach to treatment has the potential to significantly reduce lung cancer mortality. Concurrently, endoscopic ultrasound transbronchial needle aspiration has emerged as an accurate and sensitive tool for the diagnosis and staging of this disease. As knowledge of the molecular mechanisms that drive lung cancer progression increases, the amount of information that must be derived from a tumor specimen will also increase. Recent clinical studies have demonstrated that small specimens acquired by endoscopic ultrasound transbronchial needle aspiration are sufficient for molecular testing if specimen acquisition and processing are done with these needs in mind. Optimum use of this procedure requires a coordinated effort between the bronchoscopist and the cytopathologist to collect and triage specimens for diagnostic testing. When feasible, rapid onsite evaluation should be performed to assess the specimen for both diagnostic quality and quantity and to allocate the specimen for cell-block and possible immunohistochemistry and molecular studies. It is necessary for pulmonologists and bronchoscopists to understand the rationale for histologic and molecular testing of lung cancer diagnostic specimens and to ensure that specimens are acquired and processed in a fashion that provides information from small cytologic specimens that is sufficient to guide treatment in this era of targeted therapy.Keywords: lung cancer; bronchoscopy; cytology; EGFR; molecular testing Lung cancer remains the leading cause of cancer mortality in the world, with 157,000 deaths expected in the United States in 2010 (1). Despite the large death toll, there are reasons to be cautiously optimistic for a future with fewer lung cancer deaths. Recent advances in clinical and bench research directed toward diagnostics and therapy have led to significant and often dramatic impacts on patient outcomes (2). These developments suggest that a personalized approach to treating lung cancer has the potential to significantly reduce lung cancer mortality. Current standards of care for advanced non-small cell lung carcinoma (NSCLC) treatment assign therapy on the basis of histology and on the basis of epidermal growth factor receptor (EGFR) status for lung adenocarcinoma. This paradigm shift away from homogenous therapy of NSCLC converges with the increased use of bronchoscopic approaches for lung cancer diagnosis and staging, thus enhancing the important role for pulmonary physicians in lung cancer management. It is essential that the bronchoscopist understand the importance of acquiring and processing diagnostic specimens in a manner that provides sufficient information to guide treatment in this era of personalized therapy. This article reviews the rationale for acquiring specific histologic and molecular data from lung cancer biopsies, and recommends multidisciplinary procedures for specimen acquisition and processing that can optimize the yield of pulmonary diagnost...