The goal of using of oligodeoxyribonucleotides containing CpG dinucleotides (CpG DNA) as immunomodulatory agents has been realized in recent years. Therapeutic applications of CpG DNA as monotherapies and as adjuvants in combination with vaccines, antibodies, antigens and allergens for a number of disease indications are rapidly expanding, and the safety and efficacy of several first-generation CpG DNA agents are being evaluated in human clinical trials. The biological effects of CpG DNA have been known for two decades; however, only recently has a specific receptor(s) that recognizes CpG DNA and activates immune cascade been identified. A number of sequence and structural characteristics of CpG DNA and chemical modifications that influence immunostimulatory activity have been identified. In this article we summarize the recent progress in understanding the structural and chemical characteristics of CpG DNA that are significant for molecular recognition. In addition, we describe the design of second-generation CpG DNA agents, and clinical applications of first-generation agents.