The commercially available branched polyethyleneimine (PEI) with a molar mass of 25 kD (PEI-25K) is an effective in vitro vector to transfer genes, but its cytotoxicity limits its applications in bio-related research. To solve such an efficiency-versus-cytotoxicity catch-22 problem, the disulfide bond has been previously used to link less toxic short PEI chains (2 kD), but previous literature results are controversial. Recently, we found that it is vitally important to remove both carbon dioxide and water in the linking reaction as well as to control the structure of the resultant chains linked by dithiobis(succinimidyl propionate) (DSP). Under a programmable mixing of PEI and DSP, we can use laser light scattering (LLS) to in-situ monitor the linking reaction kinetics in DMSO in terms of the change of the average molar mass (M(w)). Therefore, we were able to withdraw a series of linked PEI chains with different molar masses from one reaction mixture. Two such linked PEI samples (M(w) approximately 7 kD, PEI-7K-L and approximately 400 kD, PEI-400K-L) were used to illustrate the effect of the sample preparation and the chain structure on the in vitro gene transfection and cytotoxicity. Our results reveal that PEI-7K-L is less cytotoxic and more effective in the gene transfection than both PEI-25K and Lipofectamine 2000 in the in vitro gene transfection. However, PEI-400K-L has no gene transfection efficiency even though it is non-toxic.