Objective  By comparing the transduction efficiencies of GFP and RFP reporter genes in human cell lines hMSC, Eahy926 and A549, we provide the choice of reporter genes in the regeneration medicine and the organization engineering researches. Methods  Human cell lines of hMSC, Eahy926 and A549 in vitro were respectively infected with lentiviral vectors encoding GFP and RFP reporter gene at MOI 100. After 4 days of transfection, the transduction efficiencies of GFP and RFP in each cell line were evaluated byflow cytometry. The expressive features of GFP and RFP reporters in cells were observed with confocal microscopy.  Results  We found that the transduction efficiencies of either GFP or RFP among three cell lines were very significantly difference (P<0.01). The transduction efficiencies of GFP and RFP among same cell line also was markedly varied and the difference was statistical significant (P<0.01). The RFP was concentrated expression at the subcellular localization in small population cells of Eahy926 and A549 strain. Conclusion The transduction efficiencies of GFP and RFP were evidently different among hMSC, Eahy926 and A549 cell lines.