The purpose of this study was to test quantum dots (QDs) separation by native and Tris–Glycine SDS-PAGE according to the protocols commonly used for protein analyses. To study the electrophoretic behaviour of quantum dots, ten samples of previously synthesized CdTe QDs stabilized with mercaptosuccinic acid (MSA) were used. Prior to electrophoresis the hydrodynamic diameters of QDs and zeta potentials were determined, as well as the fluorescence properties and stability of QDs in the running buffers. After verification of QDs stability and separation in native polyacrylamide gel, SDS-PAGE in gradient 4–20 % polyacrylamide gel was performed. Under UV irradiation a colour-dependent separation of QDs was observed, which was consistent with their hydrodynamic diameter distribution. The electrophoretic conditions were further optimized with respect to achieving the optimal colour separation, fluorescence stability and to minimize the time of analysis. Based on the results obtained, for further work 15 % polyacrylamide gels with SDS were used and the times (30–60 min) and voltage (100–150 V) used for separation were optimized. Under the optimal separation conditions (30 min, 100 V) the addition of MSA in the concentration range 0–4 mM was used to improve visualization of QDs with diameters in the range from 7 ± 2 to 4 ± 2 nm.