CdTe Quantum dots (QDs) are nanoparticles (2 – 10 nm) made of semiconductor materials. QDs have got very good fluorescence properties, they have got high quantum yields, big Stokes shifts, high molar extinction coefficient and they are resistant to photobleaching and chemical degradation. These characteristics predispose them for use in fluorescent labelling. They can be excited by a broad spectrum of wavelengths and on the contrary, their emission spectra are narrow and size-tuneable (from the UV to the NIR regions). Using different emission filters (535 nm, 600 nm, 700 nm), it is possible to distinguish between different QDs. QDs of different colour were prepared by microwave synthesis (50 – 130°C; 20 minutes). QDs are potentially beneficial in the imaging of the biological processes in the living organisms either in the microscopic or macroscopic level. The aim of this study was the application of QDs into the chicken muscle tissue and study of their behaviour in various depths under the surface (2, 5, and 7 mm). We investigated the differences between CdTe QDs with different emission maxima (550, 615 and 705 nm) and the limits of the usage as fluorescence probes for fluorescence in vivo imaging.