In vivo imaging system (IVIS) is a novel and rapidly expanding technology that is widely applied in life sciences, including cell tracing. IVIS is able to quantify biological events, including tumor proliferation, through counting the number of photons emitted from a specimen. PLA802-enhanced green fluorescent protein (EGFP), PLA802-monomeric cherry fluorescent protein (mCherry), RH30-EGFP and RH30-mCherry tumor cells were injected into 18 BALB/c female nude mice subcutaneously with 5×10 cells in 100 µl to quantitatively analyze EGFP and mCherry cells traced by IVIS. Inversion fluorescence microscopy revealed no transfection efficiency difference between PLA802-EGFP (95.3±1.2%) and PLA802-mCherry (95.8±1.7%), or between RH30-EGFP (94.7±2.1%) and RH30-mCherry (95.2±1.9%). Transfection did not influence the cell morphology of PLA802 or RH30. The cell migration, invasion and proliferation assay results of lentivirus-EGFP and lentivirus-mCherry revealed no significant difference prior to or following transfection. Therefore, lentivirus-EGFP and lentivirus-mCherry may serve as safety biological markers for PLA802 and RH30 cells. experiments demonstrated that lentivirus-EGFP and lentivirus-mCherry tumor luminescence signals were observed in all mice by IVIS. Hematoxylin-eosin staining and immunohistochemistry indicated that PLA802-EGFP, PLA802-mCherry, RH30-EGFP and RH30-mCherry cell lines exhibited rhabdomyosarcoma (RMS) characteristics like the maternal cells. In summary, mCherry and green fluorescent protein in human RMS PLA802 and RH30 cancer cells may be safely and stably expressed for a long time and .