A lyophilized polynucleotide composition contains at least one polynucleotide and at least one cryoprotectant, wherein the ratio of the polynucleotide to cryoprotectant is from about 0.001 to about 1.0 part by weight polynucleotide per 1.0 part by weight of the cryoprotectant. This composition also contains from about 0.5 weight percent to about (6) weight percent water, based on the total weight of the final lyophilized polynucleotide composition. The polynucleotide composition of this invention is characterized by enhanced stability, in that it retains at least 90% supercoil over a time period of at least (10) days at a temperature of about 37.degree. C. The lyophilized polynucleotide composition also has improved solubility. An improved process for lyophilization of polynucleotides employs a specific primary drying cycle, that results in the above-described stable, lyophilized polynucleotide composition.