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DNA vaccine is a third generation vaccine type based on concepts and techniques of molecular biology. It can closely mimic live infections and induce both antibody and cell mediated immune responses and thus has much potential for treating chronic viral infection and cancer. How do we transport the DNA vaccine to the right target cells in lymphoid tissues and organs? How do we achieve high and robust gene transfection efficiency while simultaneously inducing DC maturation and antigen presentation? These questions pose significant challenges and addressing them may require serious efforts in developing better biomaterials as carriers. This review is dedicated to the discussion of polymers as nanoscale carriers for the DNA vaccine. We summarize recent advances in polymer science and engineering to overcome multilevel hurdles for DNA vaccine delivery and conclude with thoughts on challenges and opportunities that may shape the future of polymers in DNA vaccination.