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Three-dimensional (3D) spheroid cell cultures of fibroblast (L929) and tumor mammary mouse (4T1) were chosen as in vitro tissue models for tissue imaging of ternary AgInS/ZnS fraction quantum dots (QDs). We showed that the tissue-mimetic morphology of cell spheroids through well-developed cell–cell and cell–matrix interactions and distinct diffusion/transport characteristics makes it possible to predict the effect of ternary AgInS/ZnS fraction QDs on the vital activity of cells while simultaneously comparing with classical two-dimensional (2D) cell cultures. The AgInS/ZnS fractions, emitting in a wide spectral range from 635 to 535 nm with a mean size from ∼3.1 ± 0.8 to ∼1.8 ± 0.4 nm and a long photoluminescence lifetime, were separated from the initial QD ensemble by using antisolvent-induced precipitation. For ternary AgInS/ZnS fraction QDs, the absence of toxicity at different QD concentrations was demonstrated on 2D and 3D cell structures. QDs show a robust correlation between numerous factors: their sizes in biological fluids over time, penetration capabilities into 2D and 3D cell structures, and selectivity with respect to penetration into cancerous and healthy cell spheroids. A reproducible protocol for the preparation of QDs along with their unique biological properties allows us to consider ternary AgInS/ZnS fraction QDs as attractive fluorescent contrast agents for tissue imaging.