The importance of cytologic techniques for investigation of respiratory conditions has been recognized since the earliest days of clinical cytology. Cytology is able to detect most of mycoses and parasitic and viral infections based on the morphologic recognition of these agents. The most relevant application of lung cytology today is in the diagnosis and management of lung cancer; approximately 70% of those cancers are diagnosed at a late stage and are unresectable. This article addresses the most common ancillary techniques, such as special stains, immunocytochemistry, and molecular testing, used to refine the cytologic diagnosis of lung cancer and to guide personalized therapy.