Recent research has led to increased concern about the potential adverse human health impacts of carbon nanotubes, and further work is needed to better characterize those risks and develop risk management strategies. One of the most important determinants of the chronic pathogenic potential of a respirable fiber is its biological durability, which affects the long-term dose retained in the lungs, or biopersistence. The present article characterizes the biodurability of single-walled carbon nanotubes using an in vitro assay simulating the phagolysosome. Biodurability is observed to depend on the chemistry of nanotube surface functionalization. Single-walled nanotubes with carboxylated surfaces are unique in their ability to undergo 90-day degradation in a phagolysosomal simulant leading to length reduction and accumulation of ultrafine solid carbonaceous debris. Unmodified, ozone-treated, and aryl-sulfonated tubes do not degrade under these conditions. We attribute the difference to the unique chemistry of acid carboxylation, which not only introduces COOH surface groups, but also causes collateral damage to the tubular graphenic backbone in the form of neighboring active sites that provide points of attack for further oxidative degradation. These results suggest the strategic use of surface carboxylation in nanotube applications where biodegradation may improve safety or add function.