In primary cultured cells including bone marrow-derived MSCs, most transfection techniques achieve very low efficiencies, generally no more than a few percent. Thus, preparing effective transfection methodologies is crucial to the success of MSC-based gene therapy. Facial amphiphiles having hydrophilic and hydrophobic groups located on two opposite faces have known to destabilize plasma membrane and enhance their permeability. To develop efficient transfection methods for MSCs, herein different types of bile acids having facial amphiphilicity were conjugated to polyethyleneimine (PEI,1.8kDa) (PEI-BA). The synthesized PEI-BA conjugates were used to transfer hypoxia-inducible vascular endothelial growth factor (HI-VEGF) gene expression vector in MSCs for the treatment of rat myocardial infarction. Although different bile acid-modified PEI conjugates showed similar ability for the formation of pDNA polyplexes with average diameters of a few hundred nanometer, there was a big difference in transfection efficiency of rat MSCs between three bile acid-PEIs (cholic acid/deoxycholic acid/lithocholic acid/conjugated PEI, PEI-CA/DA/LA). Among three conjugates, PEI-DA showed the highest transfection efficiency in rat MSCs at a weight ratio of 4. It has been known that the geometry and the distribution of hydrophilic and hydrophobic groups on facial amphiphiles including bile acids are key parameters influencing their properties, such as membrane permeability. Compared with conventional polymers, PEI-DA exhibited more than 10-fold higher transfection efficiency in rat MSCs. When PEI-DA carrier system was combined with HI-VEGF plasmid, it led to a 50-fold increase in MSC transfection efficiency without any toxicity. Furthermore, the prepared HI-VEGF-engineered MSCs (HI-VEGF-MSCs) resulted in improved cell viability, particularly during severe hypoxic exposure (1% O2) in vitro. The transplantation of MSCs genetically modified to overexpress HI-VEGF by BA-PEI enhanced the capillary formation in the infarction region and eventually attenuated left ventricular remodeling after myocardial infarction in rats. This study demonstrates the applicability of the BA-PEI conjugates for the efficient transfection of therapeutic genes into MSCs and the feasibility of using the genetically engineered MSCs in regenerative medicine for myocardial infarction.