Single-walled carbon nanohorns (SWNHs) intravenously administered to mice did not show severe toxicity during a 26-week test period, which was confirmed by normal gross appearance, normal weight gain and the lack of abnormality in the tissues on histological observations of the mice. SWNH biodistribution was influenced by chemical functionalization. Accumulation of SWNH in the lungs reduced as SWNH hydrophilicity increased; however, the most hydrophilic SWNHs modified with bovine serum albumin (BSA) were most likely to be trapped in the lungs, suggesting that the BSA moiety enhanced macrophage phagocytosis in the lungs. Clearance of some of the hydrophobic SWNHs from the lungs was observed, the mechanism of which is briefly discussed.