Translocation and localization of single-walled carbon nanotubes (SWNTs) in normal and cancerous cells have significant biomedical implications. In this study, SWNTs functionalized with different biomolecules in cells were observed with confocal laser scanning microscopy. Functionalized with PL-PEG, SWNTs were found to localize exclusively in mitochondria of both tumor and normal cells due to mitochondrial transmembrane potential, but they were found mainly in lysosomes of macrophages due to phagocytosis. However, when conjugated with different molecules, the subcellular localization of the surface-modified SWNT-PL-PEG depended on how SWNTs enter the cells: inside mitochondria if crossing cell membrane or inside lysosomes if being endocytosized. We also show that mitochondrial SWNT-PL-PEG, when irradiated with a near-infrared light, can induce cell apoptosis due to mitochondrial damages. These findings provide a better mechanistic understanding of cellular localization of SWNTs, which could lead to advanced biomedical applications such as the design of molecular transporters and development of SWNT-assisted cancer therapies.