The invention comprises stabilized polynucleotide complexes that have a cryoprotectant and are lyophilized. Cryoprotectant compounds comprise carbohydrates or sugars, preferably lactose and sucrose, but also glucose, maltodextrins, mannitol, sorbitol, trehalose, and others. Other suitable cryoprotectants include amino acids such as betaines and prolines. Polynucleotide complexes stabilized according to the invention can be used for transfection, and exhibit improved tranfection efficiency with respect to polynucleotide complexes without cryoprotection.