Adoptive transfer of donor cells in mice is widely used in research on the function and metabolism of lymphocytes. We have evaluated new approaches for quantifying and visualizing adopted cells in recipient mouse tissue. We injected spleen cells from male beta-galactosidase (LacZ) transgenic mice into female wild type mice and assessed the robustness of real-time PCR for quantifying the accumulation of the donor cells in blood and tissues of the recipient mice. The clearance of donor cells from the blood and their recruitment in lung, spleen, liver, and kidney was almost identical when obtained with amplification of the donor cell-specific LacZ or sex-determining region on the Y-chromosome (SRY) gene. We found, however, a marked difference in the PCR amplification efficiency of genomic DNA of different tissues, which should be taken into account when comparing recruitment of donor cells in different tissues. To visualize adoptively transferred cells, we used either spleen cells from transgenic mice, which express a Green Fluorescent Protein (GFP) transgene or spleen cells that had been fluorescence labeled ex vivo with CellTracker Orange. Whereas ex vivo and in vivo labeled donor cells could easily be detected in recipient mouse tissue by laser scanning confocal microscopy, only CellTracker Orange-labeled cells could be detected by conventional fluorescence microscopy due to autofluorescence in the examined tissues. Importantly, CellTracker Orange labeling did not appear to affect the blood clearance or the tissue accumulation of the donor cells. Together, the results demonstrate the usefulness of new protocols for quantifying and visualizing adoptively transferred cells by genetic tracing or fluorescence labeling.