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Semiconductor nanoparticles (quantum dots, QDs )have broad applications in novel electronic and photonic devices due to their unique optical and electronic properties. Quantum dots are used as luminophores, sensitizers and as fluorescent labels and pigments for biological cells and tissues visualization. Although nanoparticle size and shape could be determined by electron microscopy and the chemical composition could be established in general, physical properties of the similar QDs may vary significantly. In other words the structure of QD has a great impact on its properties (for instance fluorescence). In the present study we develop a method allowed to reveal compound distribution inside QD by Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS). The method is based on depth profiling capabilities of TOF-SIMS. While TOF-SIMS lateral resolution is limited to tens of nm, which is not enough for QD analysis, sub-nanometre depth resolution may be achieved with certain parameters [1-2]. Quantum dots were applied on the silicon wafers and analyzed under Bi3+ bombardment. Cesium gun was employed for depth profiling. Initially the method was tested on CdSe/ZnS core-shell nanoparticles with determined structure. Core-shell structure was observed by Se and S signals. The same parameters were applied to Mn:ZnS:CdS QDs with unknown structure. Although Cd signal was insufficient for interpretation, Mn/Zn signal ratio remains constant during the experiment. It indicates that Mn, which is dopant element, localization correlates with Zn localization in the sagittal plane. Nevertheless it does not prove that Manganese distributed uniformly in the QD. It may have “marble-like” distribution which could give the same signal pattern. Although presented study does not allow to establish precise structure of the QD it can be useful for revealing structural features of the QD by element signal correlation as it was shown for core-shells.