Most biopolymer drugs to date have been proteins. However, the ability to select nucleic acid binding species (aptamers) has led to the development of protein inhibitors and modulators that are small, readily synthesized nucleic acids. The techniques for optimizing, stabilizing, and delivering nucleic acid therapies are just beginning to be developed, but the same engineering flexibility that has so far allowed the generation of multiple, high affinity and specificity binding species appears to also apply to the methods for adapting nucleic acids to clinical applications. We review the selection and characterization of various aptamers and their applications to a variety of disease states, and then focus on the hurdles that must be overcome for the use of aptamers as both exogenously delivered drugs and as gene therapies.