Progresses in ubiquitous, embedded, and social networking and computing make possible for people in urban areas to dynamically interact with each other and with ICT devices around. This can result in a system with a very large number of agents working together in an orchestrated and self-organizing way to achieve specific urban-level goals, i.e., as if they were a “superorganism”. In this paper, we sketch the future vision of urban superorganisms and overview some emerging application areas heading towards the vision. Following, we identify the key challenges in engineering self-organizing multi-agent systems that can work as a superorganism, i.e., seamlessly involving ICT agents and human agents so to achieve some required urban level goals. Finally, we introduce the reference architecture for an infrastructure to support our future vision of self-organizing urban superorganisms.