The aim was to investigate the effect of particle size on transfection efficiency of chitosan (CS)-based nanoparticles. Nanoparticles were synthesized through complex coacervation CS with plasmid DNA (pDNA). Three kinds of pDNA/CS nanoparticles with different sizes (250, 580 and 1300 nm) were prepared by altering the adding rate and the vortexing time. The particle size, zeta potential and the stability in cultural medium were evaluated by zetasizer. The association efficiency was determined by spectrofluorophotometer. The combination of chitosan with pDNA as well as the ability to protect pDNA from nuclease degradation was analyzed by gel electrophoresis. The transfection efficiency of pDNA/CS nanoparticles in HEK293 cells was investigated by flow cytometry. Using CS grafted fluorescein isothiocyanate as a fluorescent marker, the adsorption features of the nanoparticles were visualized by fluorescence microscopy and the cellular uptake percent was quantitated by flow cytometry. The internalization process of the nanoparticles was visualized by confocal laser scanning microscopy (CLSM) using nanoparticles of the size of 250 nm. Results showed that the three kinds of pDNA/CS nanoparticles had no differences in zeta potential, association efficiency, protection ability, stability and transfection efficiency in HEK293. The nanoparticles were all adsorbed on cell surface in the form of aggregates, and similar cellular uptake percent as well as quantities were observed 4 h post-incubation with HeLa cells. CLSM images showed that the aggregates below 2 microm could be internalized by endocytosis. These results suggest that the transfection efficiency of pDNA/CS nanoparticles does not depend on particle size in the range from 250 nm to 1300 nm.