Objective The broad range of increasing applications for carbon nanotubes (CNTs) may bring hazardous exposure to humans and other biological systems. Modification of CNTs with different chemical groups was used to enhance solubility and was likely to result in different toxicity. The current study was designed to study the cytotoxicity of pristine CNTs (p-CNTs) and functionalized CNTs (f-CNTs) against vascular endothelial cells,which mediate many key biological processes in the body. Methods Vascular endothelial cells (VECs) were isolated from human umbilical veins and identified by immunochemical staining. MTT assay was employed to test the viability of the VECs exposed to different concentrations of p-CNTs or f-CNTs for up to 72 h. The mor-phology of the cells was observed under transmission electron microscope. Results It was demonstrated that both p-CNTs and f-CNTs induced decreased cell viability in a dose dependent manner, whereas neither of the medium dialyzed against p-CNTs or f-CNTs showed any cytotoxicity against the VECs. The eytotoxicity of p-CNTs was greater than that of f-CNTs after at 24 h of exposure. However, at 48 h and 72 h of exposure, f-CNTs resulted in greater decrease of cell viability as compared to p-CNTs. Transmission electron microscopic observation showed that there were much more CNT aggregates in the cytoplasm of f-CNTs treated cells than those of p-CNTs treated cells. It was also observed that the p-CNT aggregates are much more condensed than f-CNTs aggregates. Conclusion It is likely that the aggregation may play greater role in the cytotoxicity of p-CNTs, whereas the sur-face chemistry was the major factor responsible for that of f-CNTs. Increased number of f-CNTs enveloped by the cells may cause greater degree of cell damage or interfere the mass transportation in the cytoplasm, and hence in-duced increased loss of cell viability.