In this research pDNA-loaded chitosan/alginate-dextran sulfate nanoparticles with encapsulation efficiency from 83.07 to 94.71% were prepared using modified ionotropic gelation method. Encapsulated pDNA was tightly bound to polymers and protected from hydrolysis by a BamHI nuclease. All prepared nanoparticles were non-toxic for cells of HEK298 line. Moreover, chitosan/alginate-dextran sulfate nanoparticles increased proliferation of the cells in contrast to LipofectaminTM, used as a positive control for transfection. The particles prepared were effective in transfection of pEGFP-N2 plasmid into the human cells. High homogeneity of nanoparticles, reliable protection of the encapsulated DNA, and considerably high transfection efficiency along with absence of toxicity make DNA-loaded chitosan/alginate-dextran particles a suitable gene carriers in vitro and promising candidates for design of delivery systems for gene therapy.