We provide the first evidence that the size (diameter) of carbon nanotubes (CNTs) is a key factor governing their antibacterial effects and that the likely main CNT-cytotoxicity mechanism is cell membrane damage by direct contact with CNTs. Experiments with well-characterized single-walled carbon nanotubes (SWNTs) and multiwalled carbon nanotubes (MWNTs) demonstrate that SWNTs are much more toxic to bacteria than MWNTs. Gene expression data show that in the presence of both MWNTs and SWNTs, Escherichia coli expresses high levels of stress-related gene products, with the quantity and magnitude of expression being much higher in the presence of SWNTs.