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Background: To find small pulmonary nodules or ground grass nodules (GGNs) with video-assisted thoracoscopic surgery (VATS) is very difficult. There are several conventional methods to localize small nodules or GGNs, which require additional radiation exposure and may cause some complications such as pneumothorax or hemothorax. We aimed to evaluate the effectiveness and feasibility of electromagnetic navigational bronchoscopy-guided pulmonary localization in a minimally invasive thoracic surgery field. Methods: We retrospectively reviewed the medical records from a prospectively collected database of the patients who underwent ENB procedure for biopsy and/or localization of pulmonary resection at the Chungnam National University Hospital from January 2017 to January 2018. Results: A total of 37 ENB-guided dye-markings or biopsies for 37 lesions in 30 patients were performed. Thirty-two ENB-guided localizations using dye-marking for resection were performed in 25 patients. The median nodule size was 9 mm (IQR: 7–13 mm), and the median distance from the pleura was 6 mm (IQR: 3–10 mm). The failure of an ENB-guided localization was noted in 4 cases (12.5%). There was no major complication noted with the procedure, and just two patients showed mild intrabronchial bleeding stopped spontaneously. The most common lobar location was right lower lobe (11 cases, 34.4%), and all cases of localization failure were right lower lobe. A pathologic diagnosis was obtained from surgically resected specimen (not from ENB biopsy: 32 of 32 localizations, 100%), neoplastic lesions were 23 cases (72%). Of them, a primary lung cancer and metastatic lung cancer were noted in 11 cases, and in 11cases, respectively. All margins of the nodules were negative. Conclusions: The ENB-guided dye localization by a well-trained thoracic surgeon enables accurate intraoperative identification of GGN or a small pulmonary nodule, with minimal complications and enables minimally invasive surgery including single port surgery.