Carbon nanotubes (CNTs) are promising biomaterials in the medical field, especially in tissue engineering of bone. However, the use of CNTs is largely confined by its unfavorable solubility and toxicity. To improve solubility and biocompatibility of CNTs, functionalization has been proven to be an effective strategy. Although various functionalized CNTs have been extensively studied, only few CNTs have the desired qualities. We compared the toxicity of several promising functionalized multi-walled carbon nanotubes (MWCNTs) on rat bone-marrow derived stem cells (BMSCs). Cell experiments showed that while acid oxidation (AO)-MWCNTs and Raw-MWCNTs exhibited significant toxicity on BMSCs, polyethylene glycols (PEG)-MWCNTs and hydroxyapatit (HA)-MWCNTs had favorable biocompatibility and a trivial effect on BMSCs. Possible mechanisms for the cytotoxicity on BMSCs included mitochondrisome and deoxyribonucleic acid damage, increased oxidative stress and damaging of cellular membranes. Our data indicated that PEG-MWCNTs and HA-MWCNTs may be promising materials for bio-related applications.