Sustainable governance of emerging technologies such as nanotechnology is a demanding societal challenge due to the "technological throughput" of today's and tomorrow's social life. A prerequisite for sustainable governance is an integrated understanding of the factors, interdependencies and developmental potentials of the technological system under investigation. This paper presents a transdisciplinary qualitative system analysis on nanotechnology in Switzerland, integrating perspectives from science, business, government, and society. It provides basic knowledge about the systemic characteristics of nanotechnology development, considering innovation characteristics (visibility), consumers' concerns (contact) and the analogy to the GMO regulation (moratorium) as critical issues. The study affirms the method of qualitative system analysis, when applied in a transdisciplinary setting, as a useful, straightforward instrument for the early stage of sustainable governance.