Cell-penetrating peptides (CPPs) can facilitate uptake of quantum dots (QDs) for a variety of basic and applied sciences. Here we describe a method that utilizes simple noncovalent interactions to complex QDs and CPPs. We further describe methods to study uptake mechanisms of the QD/CPP complex. The inhibitor study coupled with the RNA interference (RNAi) technique provides a comprehensive approach to elucidate cellular entry of the QD/CPP complex.