Promising biomedical applications of hybrid materials composed of gold nanoparticles and nucleic acids have attracted strong interest from the nanobiotechnological community. The particular interest is owing to the robust and easy-to-make synthetic approaches, to the versatile optical and catalytic properties of gold nanoparticles combined with the molecular recognition and programmable properties of nucleic acids. The significant progress is made in the development of DNA–gold nanostructures and their applications, such as molecular recognition, cell and tissue bioimaging, targeted delivery of therapeutic agents, etc. This review is focused on the critical discussion of the recent applications of the gold nanoparticles–nucleic acids hybrids. The effect of particle size, surface, charge and thermal properties on the interactions with functional nucleic acids is discussed. For each of the above topics, the basic principles, recent advances, and current challenges are discussed. Emphasis is placed on the systematization of data over the theranostic systems on the basis of the gold nanoparticles–nucleic acids hybrids. Specifically, we start our discussion with observation of the recent data on interaction of various gold nanoparticles with nucleic acids. Further we describe existing gene delivery systems, nucleic acids detection, and bioimaging technologies. Finally, we describe the phenomenon of the polymerase chain reaction improvement by gold nanoparticle additives and its potential underlying mechanisms. Lastly, we provide a short summary of reported data and outline the challenges and perspectives.