The purpose of this study was to evaluate the diagnostic accuracy of bronchoscopy with virtual bronchoscopy (VB) navigation. Forty-two consecutive patients with ≤30-mm diameter peripheral pulmonary shadows or lesions that were difficult or impossible to identify on plain x-rays regardless of size were selected. Before bronchoscopy, multidetector computed tomography was performed, and VB images were created. Then, ultrathin bronchoscopy was carried out with VB navigation followed by conventional 4-mm diameter bronchoscopy. Thirty-seven patients were finally enrolled. There were 12 re-examination cases in which earlier conventional bronchoscopy was nondiagnostic. Diagnosis was established in 28 patients (25 malignant and 3 benign lesions), with the diagnostic yield of 75.7% (sensitivity 86.2%, specificity 62.5%, positive predictive value 89.3%, negative predictive value 55.6%, and accuracy 81.1%). The diagnostic yield for lesions of diameter ≤20 mm, 21 to 30 mm, and ≥31 mm were 76.9%, 76.5%, and 71.4%, respectively, for all patients, and 90%, 84.6%, and 83.3%, respectively, for malignant cases. The diagnostic yield in patients who underwent re-examinations was 83.3% for all cases and 88.9% for malignant cases. Three patients had completely invisible shadows on x-ray fluoroscopy and all of these cases were diagnosed on bronchoscopy. No statistically significant difference was observed between the diagnostic yield for the different sizes, pathology, and number of bronchoscopies required. Bronchoscopy with VB navigation yielded high accuracy even for small peripheral pulmonary nodules and shadows that were difficult or impossible to identify on plain x-rays, even for patients in whom earlier conventional bronchoscopy was nondiagnostic.