Quantum dots (QDs) are luminescent nanoparticles with unique optical properties that have been exploited for single-cell and whole-animal imaging. When coated with proteins or biocompatible polymers, QDs are not deleterious to cells and organisms. However, when QDs are retained in cells or accumulated in the body for a long period of time, their coatings may be degraded, yielding "naked" QDs. Here, we show that "naked" QDs induce damage to the plasma membrane, mitochondrion, and nucleus, leading to cell death. Reactive oxygen species (ROS) are important players in mediating QD-induced cellular damage. QD-induced cytotoxicity can be reduced or even eliminated without covalent binding of protective agents to the QD surface. Results from these studies suggest the critical role of several subcellular compartments in QD-induced cytotoxicity and point toward multiple molecular targets in nonclassical apoptosis.