The increasing knowledge about the roles of different genes involved in both acquired and hereditary diseases has made gene delivery an ever promising weapon in disease treatments. Different gene delivery strategies have been investigated in the past three decades among which non-viral gene delivery has received increasing attention due to a number of evident benefits. Delivery of a therapeutic gene to the targeted site in non-viral gene delivery is often aided by vectors such as polymers, lipids, peptides and nanoparticles, but their efficiencies and side effects such as cytotoxicity have stimulated extensive studies to explore how these effects can be balanced at the molecular-cell levels. Successful treatment strategies will ideally work on the basis of high transfection efficiency, low cell toxicity and the minimisation of other possible side effects. The vectors must overcome a number of physical and biological barriers after systemic or local administration. This review focuses on the molecular biophysics underlying non-viral gene delivery using different molecular vectors. A number of representative scientific studies will be introduced to demonstrate the relationships between the physicochemical properties of the DNA/vector complexes and their transfection efficiencies.