Fluorescent semiconductor nanocrystals called quantum dots (QDs) have gained attention in biomedical applications, including imaging, molecular tracking, and drug delivery, due to their unique optical properties. However, their use is limited because of safety issues. This study was aimed at assessment the acute toxicity of QDs with different core chemical compositions and surface charges in mice. In addition, the immunotoxicity of CdSe/ZnS QDs was estimated. CdSe/ZnS, PbS/CdS/ZnS, and CuInS2/ZnS QDs were synthesized and modified with PEG derivatives. The hydrodynamic diameters and surface charges of solubilized QDs were characterized. The QD acute toxicity has been shown to depend on both surface charge and core composition. The immunotoxicity of CdSe/ZnS-PEG-OH QDs in mice was assessed after a single intravenous administration of 0.2 LD100 of the QDs. The QDs have been found to increase the spleen weight and cause spleen, thymus, and bone marrow cell depletion. However, these changes are reversible. A transient increase in the levels of proinflammatory cytokines (MCP1 and IL-6) indicates an acute inflammatory response to a single low dose of QDs. Thus, systemic comparative analysis of QD toxicity has shown how the QD core composition and surface properties affect living organisms.