Gold nanorods (Au NRs) that absorb near-infrared (NIR) light have great potential in the field of nanomedicine. Photothermal therapy (PTT), a very attractive cancer therapy in nanomedicine, combines nanomaterials and light. The aim of this study was to elucidate the molecular mechanism involved in Au NR-mediated cytotoxic, genotoxic, and other biological responses, in the presence or absence of NIR irradiation. Specifically, cell death mode, generation of reactive oxygen species, DNA damage, apoptotic gene expression, and cell morphological changes induced by Au NRs under NIR irradiation were evaluated in cancer cells. In human lung adenocarcinoma epithelial cells (A549 cells), mild necrosis via DNA damage was induced by NIR responsive Au NRs. Unlike in the cancer cells, cell viability of normal human lymphocyte was not affected by the combined treatment of Au NRs and NIR irradiation. This study delineates differential cytotoxic and genotoxic susceptibility of cancer and normal cells during photothermal treatment of Au NRs. In conclusion, our results suggest that the photothermal cyto-/genotoxic activity of Au NRs is an effective method for cancer therapy in human lung cancer cells.