The development of natural or synthetic polycations able to interact with nucleic acids and condense them into nanoparticles known as polyplexes, faces several unresolved challenges at the cellular level. Key issues include the intracellular trafficking of polyplexes, the endosomal escape and the release of nucleic acids into the cytosol, which are considered major bottlenecks for efficient protein expression. Here, we aim at gaining fundamental insights into the stability of polyplexes in biological media and their uptake and intracellular trafficking, while correlating data of the expression of reporter protein with both the molecular characteristics of various poly(ethylenimines) (PEI) and the physicochemical characteristics of PEI/peGFP-C3 polyplexes. For this, we chosen four samples of PEI, selected as a model polycation, with different molecular weights (Mw = 0.8, 20, 25 and 60 kg/mol) and structures (linear and branched). We found that the in vitro and in vivo stability of PEI/peGFP-C3 polyplexes, their cell internalization and transfection efficiency is dependent on the variation of polycation Mw and structure, as well as the intrinsic properties of polyplexes, such as the charge ratio (R=[N+]/[P-]). A relation between the percentage of positive cells to green fluorescent protein (GFP) and the amount of internalized nucleic acid (cyanine 5-peGFP-C3) allowed revealing the molecular characteristics of PEI promoting both higher both cell internalization and GFP expression on HEK293T cells. In the long term, the outcome of this work will be to propose guidelines to help design more effective, and less cytotoxic non-viral gene carriers with a great potential for new therapeutic applications.