The present work addresses the development and characterization of ε-Poly-L-Lysine/pDNA polyplexes and evaluation for their improved transfection efficacy and safety as compared to polyplexes prepared using Poly-L-Lysine and SuperFect®. Self-assembling polyplexes were prepared by varying the N/P ratio to obtain the optimum size, a net positive zeta potential and gel retardation. The stability in presence of DNase I and serum was assured using gel retardation assay. Their appreciable uptake in MCF-7 and 3.5, 3.79 and 4.79-fold higher transfection compared to PLL/pDNA polyplexes and 1.60, 1.53 and 1.79-fold higher transfection compared to SuperFect®/pDNA polyplexes in MCF-7, HeLa and HEK-293 cell lines respectively, affirmed the enhanced transfection of ε-PLL/pDNA polyplexes which was well supported with in vivo transfection and gene expression studies. The <8% in vitro hemolysis and >98% viability of MCF-7, HeLa and HEK-293 cells in presence of ε-PLL/pDNA polyplexes addressed their safety, which was also ensured using in vivo toxicity studies, where hemocompatibility, unaltered levels of biochemical markers and histology of vital organs confirmed ε-PLL to be an effective and safer alternative for non-viral genetic vectors.