Cationic polyphosphoesters (PPEs) with different side-chain charge groups were designed and synthesized as biodegradable gene carriers. Poly(N-methyl-2-aminoethyl propylene phosphate) (PPE-MEA), with a secondary amino group (-CH(2)CH(2)NHCH3) side chain released DNA in several hours at N/P (amino group of polymer to phosphate group of DNA) ratios from 0.5 to 5; whereas PPE-HA, bearing -CH(2)(CH2)(4)CH(2)NH(2) groups in the side chain, did not release DNA at the same ratio range for 30 days. Hydrolytic degradation and DNA binding results suggested that side chain cleavage, besides the polymer degradation, was the predominant factor affected the DNA release and transfection efficiencies. The side chain of PPE-MEA was cleaved faster than that of PPE-HA, resulting poor cellular uptake and no transgene expression for PPE-MEA/DNA complexes in COS-7 cells at charge ratios from 4 to 12. In contrast, PPE-HA/DNA complexes were stable enough to be internalized by cells and effected gene transfection (3400 folds higher than background at a charge ratio of 12). Interestingly, gene expression levels mediated by PPE-MEA and PPE-HA in mouse muscle following intramuscular injection of complexes showed a reversed order: PPE-MEA/DNA complexes mediated a 1.5-2-fold higher luciferase expression in mouse muscle as compared with naked DNA injection, while PPE-HA/DNA complexes induced delayed and lowered luciferase expression than naked DNA. These results suggested that the side chain structure is a crucial factor determining the mechanism and kinetics of hydrolytic degradation of PPE carriers, which in turn influenced the kinetics of DNA release from PPE/DNA complexes and their transfection abilities in vitro and in vivo.