A new method of marking small pulmonary nodules situated deep within the visceral pleura using a transbronchial approach has been developed. Once the tip of the sheath catheter has passed the tumor and reached the visceral pleura, as confirmed by computed tomography fluoroscopy, indigo carmine is injected through a bronchoscope into the lung parenchyma just beneath the visceral pleura. No complications related to the procedure were experienced. The dye-marking procedure enabled the nodules to be precisely located. This technique can provide appropriate guidance when used in conjunction with video-assisted thoracic operations.