As nanomaterials are developed and applied, their potential for health hazards needs to be determined. In the present study, we used commercial nude multi-walled carbon nanotubes (MWCNTs) trimmed to a short length (50–200 nm; s-MWCNTs) and synthesized functionalized MWCNTs with polyethylene glycol (PEG) (s-MWCNTs-PEG). We then studied the toxic effects of s-MWCNTs and s-MWCNTs-PEG on cultured cells and in a mouse model. Peripheral haemograms and various biochemical markers of the heart, liver and kidney were measured. We found no toxicity of either type of nanotube on the viability of human SKBR-3 breast carcinoma cells or control cells. There were no differences in vivo on inflammatory responses, the coagulation system, haemograms or vital organ functions between the test and control groups. Additionally, we found no toxicity of these nanotubes on male mouse sperm production or mutagenesis in the long term. In conclusion, both s-MWCNTs and s-MWCNTs-PEG displayed good in vitro and in vivo biocompatibility, making future applications in biology and clinical therapy as a carrier for drug delivery feasible. Copyright © 2012 John Wiley & Sons, Ltd.