A surface-mediated gene transfer system using biocompatible apatite-based composite layers has great potential for tissue engineering. Among the apatite-based composite layers developed to date, we focused on a DNA-lipid-apatite composite layer (DLp-Ap layer), which has the advantage of relatively high efficiency as a non-viral system. In this study, various lipid transfection reagents, including a newly developed reagent, polyamidoamine dendron-bearing lipid (PD), were employed to prepare the DLp-Ap layer, and the preparation condition was optimized in terms of efficiency of gene transfer to epithelial-like CHO-K1 cells in the presence of serum. The optimized DLp-Ap layer derived from PD had the highest gene transfer efficiency among all the apatite-based composite layers prepared in this study. In addition, the optimized DLp-Ap layer demonstrated higher gene transfer efficiency in the presence of serum than the conventional particle-mediated systems using commercially available lipid transfection reagents. It was also shown that the optimized DLp-Ap layer mediated the area-specific gene transfer on its surface, i.e., DNA was preferentially transferred to the cells adhering to the surface of the layer. The present gene transfer system using the PD-derived DLp-Ap layer, with the advantages of high efficiency in the presence of serum and area-specificity, would be useful in tissue engineering.