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Autologous bone marrow mononuclear progenitor cells (ABMCs) are now being used for several regenerative medicine studies, but questions remain on the fate and function of the injected ABMCs. The ability to track the cells within animals is important in understanding the regeneration process, and both quantum dots (Q-dots) and the organic dye CM-DiI have been used frequently in cell tracking studies. Since there has not been a comparative analysis of Q-dots and CM-DiI for labeling ABMCs, the aim of the following study was to examine these probes for their ability to label ABMCs and to determine if the labeling affected the ABMC function. We found that ABMCs were easily labeled with either Q-dots or CM-DiI, with the CM-DiI being faster to load within the cells. Both Q-dots and CM-DiI could still be detected in the ABMCs after 10 days in culture. The loading of the ABMCs with CM-DiI had no effect of the ABMCs to form colonies in a CFU-F assay or on cell proliferation over two weeks. The labeling of the ABMCs with Q-dots had a small but significant inhibitory effect on CFU-F formation as well as inhibition of cell proliferation at two weeks. There was no effect of Q-dots on cell viability immediately after labeling. In summary, both Q-dots and CM-DiI can be used to label ABMCs, but CM-DiI was found to be more advantageous due to its faster loading time, ease of use, and lack of effect on colony formation and proliferation.