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Apatite samples from rare-metal mineralization were investigated by a combination of cathodoluminescence (CL) microscopy and spectroscopy, microchemical analysis and trace element analysis. Internal structures revealed by CL can be related to variations in the crystal chemistry and may sometimes reflect changes in the composition of the mineralizing fluids.Apatite from mineralization related to alkaline rocks and carbonatites (Type 1) typically exhibits relatively homogeneous blue and lilac/violet CL colours due to activation by trace quantities of rare earth element ions (Ce3+, Eu2+, Sm3+, Dy3+ and Nd3+). These results correlate with determined trace element abundances, which show strong light rare earth element (LREE) enrichment for this type of apatite. However, a simple quantitative correlation between emission intensities of REE3+/2+ and analysed element concentrations was not found.Apatite from P-rich altered granites, greisens, pegmatites and veins from Sn-W deposits (Type 2) shows strong Mn2+-activated yellow-greenish CL, partially with distinct oscillatory zoning. Variations in the intensity of the Mn2+-activated CL emission can be related either to varying Mn/Fe ratios (quenching of Mn activated CL by Fe) or to self-quenching effects in zones with high Mn contents (>2.0 wt.%). The REE distribution patterns of apatite reflect the specific geological position of each sample and may serve as a “tracer” for the REE behaviour within the ore system. Although the REE contents are sometimes as high as several hundred parts per million, the spectral CL measurements do not exhibit typical REE emission lines because of dominance of the Mn emission. In these samples, REE-activated luminescence is only detectable by time-resolved laser-induced luminescence spectroscopy.Both types of apatite (Type 1 in the core and Type 2 in the rim) were found in single crystals from the Be deposit Ermakovka (Transbaikalia). This finding proves the existence of two stages of mineralization within this deposit.