Targeted delivery to the cell nucleus can enhance the efficiency of drugs with nuclear site of action (some anti-cancer agents, DNA drugs, etc.), and can reduce their toxicity. Such targeting can be attained using nano-drug delivery systems (nano-DDSs) decorated with nuclear targeting sequences (such as nuclear localization sequence peptides, NLS). Several types of nano-DDSs decorated with NLS peptides were designed, but their investigation usually did not include quantitate analysis of the decoration efficiency and its correlation with the nano-DDSs intracellular localization. Thus, the major mechanisms and limiting factors of the nano-DDSs nuclear targeting are largely unknown yet. In this study, we report quantitative data for specific nano-formulation (CdSe-ZnS quantum dots) that include the efficiencies of its decoration with NLS residues and of its nuclear and perinuclear targeting, and demonstrate correlation between these parameters. For instance, QDs decorated with 83, 246, and 265 NLS peptides accumulated efficiently in the nucleus of HeLa cells or its vicinity (an average of 30.4%, 43.3%, and 49.0% of the intracellular QDs, respectively). On the other hand, QDs decorated with 63, 231, and 308 scrambled peptides accumulated in the nucleus of HeLa cells or its vicinity to a much lower extent (an average of 17.3%, 21.1%, and 25.5% of the intracellular QDs, respectively). Thus, results of our study provide important insights into the structure-activity correlations (i.e., the relationships between the formulation properties and the intracellular fate of nano-DDSs) of nuclear-targeted drug delivery. We plan to apply the research tools that were developed in the course of this and our previous studies to investigate the nuclear and perinuclear targeting activities of different NLS sequences, and to investigate the effects of nano-DDSs size, charge, shape, decoration efficiency with nuclear targeting sequences, and other structural factors on nuclear and perinuclear targeting efficiency.