The ciliated tracheobronchial epithelium plays an important role in the excretion of inhaled dust. While many reports indicate that inhaled multi-walled carbon nanotubes (MWCNT) induce inflammation and proliferative changes in the lung and pleura, their effects on the upper airway have not been reported. Two different types of MWCNTs, MWCNT-L (8 µm in length and 150 nm in diameter) and MWCNT-S (3 µm in length and 15 nm in diameter), were examined for their effect on the trachea as well as the bronchus and lung. In vitro, the movement of the cilia of primary tracheal epithelial cells was impaired by treatment with the 2 MWCNTs. Rats were treated with 0.3 ml of a 250 µg/ml suspension of MWCNTs on days 1, 4, and 7, and sacrificed on day 8. Extensive loss of ciliated cells and replacement by flat cells without cilia was observed in the trachea. Deposition of MWCNTs and occasional squamous cell metaplasia were found in the regenerative granulation tissue. The proportion of the lesion to the transverse section of the trachea was vehicle, 0; MWCNT-L, 27.2 ± 10.5; MWCNT-S, 32.1 ± 15.8 (both MWCNTs, p < 0.001 vs vehicle). The amount of cilia showed significant decrease in the MWCNT-L treated rats (p < 0.05). In contrast to the trachea lesions, the number of inflammatory foci in the lung was greater in the MWCNT-S than in the MWCNT-L treated rats. Our results indicate that both MWCNTs caused extensive damage to the ciliated epithelium of the trachea. This damage may prolong the deposition of inhaled MWNCT in the lung.