Molecular conjugates are nanometer-sized entities consisting of synthetic materials (lipids, polycations, targeting agents, and so on) and nucleic acids. These composites are delivery vehicles that function to provide the transport of nucleic acids to sites of action. Recently, great progress has been made in the construction of these nonviral delivery vehicles and the understanding of how they function in cells and animals. Here, we review some of the important issues in assembling molecular conjugates and understanding their behavior in biological fluids, cells, and animals. One of the largest challenges in the field of molecular conjugates is how to integrate the components into a workable system that exploits the combined attributes of the components without suffering losses due to the assembly of the system. We discuss some of the difficulties involved in the assembly of a functioning delivery system for in vivo use.