A novel strategy for gene delivery using biocleavable polyrotaxanes, in which dimethylaminoethyl-modified alpha-cyclodextrins (DMAE-alpha-CDs) are threaded onto a poly(ethylene glycol) (PEG) chain capped with benzyloxycarbonyl-L-tyrosine via disulfide linkages (DMAE-SS-PRX), involves the formation of a stable polyion complex (polyplex) against a counter polyanion and the intracellular plasmid DNA (pDNA) release from the polyplex accompanied by the supramolecular dissociation of DMAE-SS-PRXs. In this study, we prepared biocleavable polyrotaxanes with different numbers of threading alpha-CD and amino (DMAE) groups to enhance the transfection activity of DMAE-SS-PRXs. 29DMAE-alpha18-SS-PRX, in which the numbers of alpha-CD molecules and amino groups were 18 and 29 respectively, exhibited a high transfection activity compared with other PRXs. The transfection activity of DMAE-SS-PRXs seems to be related to the efficacy of pDNA release from those polyplexes, which was controlled by the number of alpha-CD and/or amino groups in the polyrotaxane carrier. Most of the DMAE-SS-PRX polyplexes released the pDNA only in the presence of both 10 mM DTT and of the counter-polyanion, as expected, except for 14DMAE-alpha18-SS-PRX, which released pDNA in the absence of dextran sulfate once the DTT had been added to the polyplex solution. The transfection activity of 14DMAE-alpha18-SS-PRX was significantly lower than that of 29DMAE-alpha18-SS-PRX regardless of the above features. Confocal laser scanning microscopic (CLSM) observation suggested that the specific result for 14DMAE-alpha18-SS-PRX might be due to a premature release of pDNA from the most dissociative 14DMAE-alpha18-SS-PRX polyplex in the cytosol. Therefore, transfection activity seems to be related to an appropriate timing of pDNA release.