Thoracoscopic resection of small subsolid nodules is challenging and requires preoperative localization. We investigated the efficacy, safety, and factors affecting accuracy in localizing pulmonary nodules with electromagnetic navigation bronchoscopy (ENB)-guided dye marking.Patients with small subsolid nodule(s) who underwent thoracoscopic resection after ENB-guided dye marking were retrospectively reviewed. Dye marking was performed at the nearest pleura and the localized nodule(s) was resected thoracoscopically. Efficacy was evaluated by success rates of dye marking and resection of nodules. Navigation accuracy was represented by target distance, which was the closest distance between target and the tip of locatable guide. Factors affecting target distance were evaluated by linear regression analyses.Twenty-nine ENB-guided dye markings were done for 24 nodules in 20 patients. The success rate of the dye marking and nodule localization were 93.1% (27/29) and 95.8% (23/24), respectively. Twenty-three nodules were completely resected thoracoscopically without conversion. There were no ENB-related complications: pneumothorax or bronchopulmonary hemorrhage. Nine targets were in the upper, 14 in the middle, and 6 in the lower zone. Even though navigation time was longer in the upper zone, target distance showed no significant inter-zone difference. Approach angle was the only significant predictor for target distance (0-45°, estimate = -1.24, P = .01; 45-90°, estimate = -1.26, P = .006; reference = ≥90°).Localization with ENB-guided dye marking is effective and safe for thoracoscopic resection of small subsolid nodules. For better performance, a pathway with smaller approach angle (<90°) should be selected to increase the navigation accuracy.