With the development of Au nanorods for a number of biomedical applications, understanding their cellular responses has become increasingly important. In this study, we systematically evaluated the cellular uptake behaviour and cytotoxicity of Au nanorods with various surface coatings, including organic cetyltrimethylammonium bromide (CTAB), poly(sodium 4-styrenesulfonate) (PSS), and poly(ethylene glycol) (PEG), and inorganic mesoporous silica (mSiO2), dense silica (dSiO2), and titanium dioxide (TiO2). The cellular behaviour of Au nanorods was found to be highly dependent on both the surface coating and the cell type. CTAB-, PSS-, and mSiO2-coated Au nanorods exhibit notable cytotoxicity, while PEG-, dSiO2-, and TiO2-coated Au nanorods do not induce cell injury. Optical imaging studies indicated that the cell type plays a preferential role in Au nanorod cellular uptake. Higher cellular uptake of Au nanorods was seen in U-87 MG, PC-3, MDA-MB-231, and RAW 264.7 cells, as opposed to HepG2 and HT-29 cells. In addition, Au nanorod cellular uptake is also highly affected by serum protein binding to the surface coating. mSiO2-, dSiO2-, and TiO2-coated Au nanorods show significantly higher cellular uptake than PSS- and PEG-coated ones, which results in a better photothermal ablation effect for Au nanorods with the inorganic surface coatings. Our study provides valuable insights into the effects of the surface modification on the biocompatibility, cellular uptake, as well as biomedical functions of Au nanorods.