This paper introduces a new experimental city generation, assembly and development platform, the urban mutations platform. We describe in detail a methodology for modeling urban systems and their dynamics, based on self-organization principles. The urban area is seen as an organism comprised of different “body parts”, the urban subunits. Upon creation of an initial 3D urban environment, it is possible to add to the subunits the so-called mutations, i.e. structural and functional components that can have beneficial or detrimental effects to the future city development. After addition of the mutations we allow the city to reorganize itself and observe possible changes in the urban configuration. These changes can be directly correlated to the added mutations and their urban qualities and allow us to probe the effect that different structural and functional elements have on the dynamic behaviour of the city, when placed at specific locations.