In recent years, nanoscale self-assembled structures have attracted ever increasing attention because of their potential to act as molecular templates for the synthesis of novel materials, delivery vehicles for therapeutic agents, and compartments defined at the molecular level that provide environmental conditions conducive to specific chemical reactions. In this review, we will focus mostly on this latter application. Amphiphiles that self-assemble to yield nano-compartments such as micelles, reverse-micelles and liposomes, have been used to build nanoscale reactors that can effect chemical reactions through spatial co-localization of the reacting species. The reacting species may include the compartment building amphiphiles themselves. These nano-compartments provide not only the conditions for the reaction to occur, but also allow the buildup of complex reaction networks by retaining primary reaction products which may in turn be capable of additional reactions. Ultimately, such complex systems could also serve as starting points for minimal artificial cells, i.e. protocells which would be highly simplified versions of biological cells and which might be engineered for specific tasks related to therapeutic and diagnostic applications. We will report on advances in the design of these chemical self-assembled systems and the challenges that still lie ahead.