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Gene therapy is a promising strategy for the treatment of various diseases. Polyethylenimine (PEI) has received considerable attention for gene delivery applications due to their appropriate properties. However, their toxicity has raised concerns which cause to be used with cautious. This study aimed to prepare different complexes of PEI/DNA and evaluate their parameters affecting in vitro cytotoxicity. Also, apoptosis rate was measured to determine the mechanism of cell toxicity.The complexes were prepared through conjugation and characterized using dynamic light scattering, MTT and flow cytometry techniques.The particles' size was from 81 nm to 2785 nm and was increased in the HBS buffer compared to HBG buffer. In the case of branched PEIs, the size of particles was inversely associated with molecular weight. The cytotoxicity results showed that linear 250 KDa PEI was non-toxic whereas branched PEIs with lower molecular weights showed toxicity effects in a concentration dependent manner. Also, the cytotoxicity effects of branched PEIs were proportional with carrier/plasmid (C/P) ratio and were more for the polyplexes prepared in HBG buffer compared to HBS buffer after 24 h incubation. Flow cytometry results confirmed that apoptosis is the main mechanism of cell toxicity produced by polyplexes.The results showed the effect of PEI size on its cytotoxicity. Also, the toxicity effects of PEI-derived polyplexes in vivo environment was evaluated.