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Background: To compare the diagnostic positive rate and complication rate between the electromagnetic navigation bronchoscopy (ENB) technique and computed tomography (CT)‐guided lung puncture for the biopsy of lung nodules located in the middle of an anatomic lung segment. Methods: Electronic medical records of 114 patients who underwent lung nodule biopsy between June 2021 and June 2022 were retrospectively evaluated. In all patients, the nodules were located in the middle third lung segment. To compare the diagnostic positive and complication rates between the two biopsy modalities performed in this lung region, clinical data, complication rates, nodule pathology, and imaging results were reviewed based on nodule characteristics retrieved from the electronic medical records. Results: Ninety‐three patients underwent CT‐guided lung puncture, while the remaining 21 patients underwent the ENB technique. No significant difference was observed in the diagnostic positive rate between the two groups (73.6 and 76.1%, respectively). In the CT‐guided lung puncture group, pneumothorax incidence, tube placement, postoperative hemorrhage, and symptomatic hemorrhage rates were 16.1, 6.5, 6.5, and 1.1%, respectively. In contrast, no complications occurred in the ENB group. Conclusions: The ENB technique is a safe and effective method for performing biopsies of pulmonary nodules with a diagnostic positive rate comparable to that of CT‐guided lung puncture and with a lower postoperative complication rate. [ABSTRACT FROM AUTHOR]