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Nanocrystals are interesting for all kind of labeling experiments in biology. For investigating biological processes, it is important to know the limits and possible side effects of the inorganic compounds that are used as probes. We applied CdSe-nanocrystals as markers in fluorescence microscopy experiments, to investigate the cell uptake of CdSe-nanocrystals versus their chemical functionalization. In addition, the application of CdSe-nanocrystals in an invasion assay for cancer cells is presented. A systematical investigation of the toxicity of nanocrystals was done, where the death of living cells (NRK-fibroblasts) was used to find the critical concentration of the nanocrystals dependent on their chemical functionalization.