Objective Convex probe endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA) is a minimally invasive technique with high sensitivity in the mediastinal staging of non-small cell carcinoma (NSCLC). In recent years, molecular testing has been developed to study genetic mutations in NSCLC. There are studies revealing improved survival in advanced NSCLC using targeted therapy as the first-line treatment in these patients. The aim of this study was to evaluate the adequacy of EBUS-TBNA in providing adequate size specimens for EGFR, ALK and ROS1 genetic mutation analysis in patients with adenocarcinoma or not otherwise specified (NOS) lung cancer. Materials and Methods Charts of patients diagnosed with lung adenocarcinoma or NOS via EBUS-TBNA were retrospectively reviewed. Information on patient demographics, number of lymph nodes sampled, their size and location, targeted gene mutations and the adequacy of the material sampled for the molecular testing was recorded. Results A total of 114 patients were included in the study, adenocarcinoma 86 (75%) and NOS 28 (25%). EGFR gene mutation was studied in all of the patients included in the study while ALK in 113 and ROS1 in 98. The material adequacy ratios for EGFR gene mutation, ALK and ROS1 rearrangements were found to be 88.6%, 93.8% and 91.8%, respectively. EGFR gene mutation, ALK and ROS1 rearrangements were found positive in 13 (11.4%), 9 (8%) and 1 (1%) patients, respectively. Conclusion The study demonstrated that EBUS-TBNA provides adequate material for mutation analysis in patients with newly diagnosed adenocarcinoma or NOS lung cancer.