Abstract: Cities are becoming a power of human development and this has made a problem of optimal and sustainable use of city territory. In 1987 Gro Harlem Brundland commission suggested to make sure a better life quality for current and future generations and paradigm of sustainable and balanced development was aroused on this background. However urban planners do not have a solid attitude on which factors most influence the level of life quality in the cities. This is because factors of market, inertia of development and complexity of urban structure make negative environment to realization of sustainable and balanced development. Sustainable and balanced development can be reached only by regulative management. It is planned by establishing functions of city territories. Nevertheless in the most of countries mono-functional zoning is dominant, what makes set of a single function and this one-way use makes overuse of territory. Poly-functional zoning is an opportunity to follow principles of sustainable development, because withdrawal of zoning can establish all functions. This can impoverish territory in different cultural, environmental, economic, infrastructural aspects. Sustainable development studies are performed as indicators of pollution, energy, environment studies, but are mostly out of sight regulation of urban functions and management. Spatial integrity was dismissed as a part of mono-functional zoning. Therefore in this article we analyze city structure and zoning, which are influenced by permanent material stream. The analysis is based on the idea of metabolistical analysis of the city. In biology metabolism is a unit of chemical reaction in each cell. That let cells to grow, to multiple, to react to environment, to move. This some analogy is used in metabolistical research of the cities and lets us understand how to develop cities in a sustainable and balanced way. Cities transform energy (minerals, environment and information) to antropogenized system with human biomass and their ideas, and with formed unacceptable object (waste). This is the system of input, recast, storage and output, which is like a fusion of social, economic, technical and landscape processes. They form characteristic of functional zones and priorities of the sustainable use of the zone. We recommend that poly-functional zones can be show by territorial graphs methods. As an example of such methodological approach results of poly-functional zoning research in Kaunas city are presented.