Lung cancer has the largest number of lives for the global pattern of cancer death. However, the percentage of the cancer treatment is too low. Gold nanoparticles have a widely range in terms of biomedical applications in diagnosis, imaging because of their unique optical properties, simple synthesis techniques, biocompatibility and suitable for easy surface change. Redox reactions in the mitochondria generates a potential called as mitochondria membrane potential. The aim of the study is to design mitochondria targeted gold nanorods and to observe how the designed gold nanorods effects the mitochondria membrane potential by targeting the mitochondria on A549 and BEAS-2B cell lines. Gold nanorods were utilized by seed growth mediated method and the surface bioconjugation was performed with triphenyl phosphonium cation as a mitochondria targeted molecule. Poly (sodium-p-styrene sulfonate) was used to prevent aggregation during the bioconjugation process. Gold nanorods which had 30 nm x 10 nm in length and diameter depending on SEM images had well-defined absorption bands 513 nm and 774 nm in wavelength. Mito-pot analysis with the fluorescent intensity ratio and colocalization analysis with light intensity for targeting gold nanorods to mitochondria showed that the accumulation on mitochondria for TPP-GNR was higher than PSSGNR. TPP-GNR was more toxic than PSS-GNR for both of cell lines by investigations of MTT viability test. TPP-GNR targeted to mitochondria and it affected fundamental cellular functions in mitochondria. To concluded that accumulation on mitochondria was accomplished for TPP-GNR and the decreasing of mitochondria membrane potential was observed on this study.