Occasionally, we have difficulty in diagnosing small peripheral pulmonary nodules. However, efforts have been made to resolve this problem. For instance, computed-tomography (CT), positron emission tomography (PET), flexible bronchoscopy examination (BF), and video-assisted thoracic surgery (VATS) have been performed to investigate such nodules. We have used endobronchial ultrasonography with a guide-sheath (EBUS-GS) for BF examination, and recently applied the virtual reality technique "virtual bronchoscopy (VB)". Here, we present a case in which a combined technique with VB and EBUS-GS was useful. The patient was a 54-year-old man with a persistent cough and chest pain. Small nodules were seen in the bilateral lungs on the chest CT taken at the local hospital. A slight increase in the CEA level (6.1 ng/ml; normal level < 5.0 ng/ml) was shown as well as an uptake in the latter term on PET. As a result, he was referred to our hospital for a detailed work-up. We applied VB to confirm the location of the tumor, which allowed us to approach the lesion easily. Furthermore, we precisely localized the lesion using EBUS-GS. Then a biopsy was performed, which demonstrated bronchiolitis obliterans organizing pneumonia (BOOP). As seen in this case, combining VB and EBUS-GS seems beneficial for diagnosing peripheral pulmonary nodules.