Cytotoxicity and genotoxicity of plasma-modified multi-walled carbon nanotubes (MWCNTs), including hydroxyl-MWCNTs (MWCNT-OH), carboxyl-MWCNTs (MWCNT-COOH) and pristine MWCNTs, with human ocular cells (e.g. retinal pigment epithelium (RPE) cells) have been studied in this work. The addition of MWCNT-based materials caused few change in cell morphology while the presence of MWCNTs was observed inside the cells using transmission electron microscopy (TEM), suggesting possibility of MWCNTs passing through the cell membranes without damaging cells. Cell viability measurements suggested that MWCNT-COOH exhibited better biocompatibility than other MWCNT materials studied in this work. Lactate Dehydrogenase (LDH) release level was found to be less than 30% with all types of MWCNT-based materials. Reactive Oxygen Species (ROS) generation was visible but not severe with addition of nanotubes. A smaller oxidative stress level was obtained from MWCNT-COOH. Cell apoptosis was found to be less than 1.5% with addition of MWCNT-based materials. Particularly MWCNTs were found to be swallowed by cells and released by cells after 72 h without damaging cells, which may be considered as a potential vector for ocular genetic diseases. Plasma modification of MWCNTs particularly with -COOH was found to be an efficient way to improve ocular biocompatibility of MWCNTs, suggesting a fast and useful way to modify MWCNTs for applications in areas such as biology and biomedicine.