The current trend of green buildings is reflected in the construction of administration buildings and of residential complexes. There is a non-profit organization Czech Green Building Council in the Czech Republic, which integrates different companies linked to economics to transform the current method of construction for green energy and healthier building. On the one side stands the cost of the green building, but on the other hand, there stand operating costs of the life cycle of the buildings and they have considerable influence in deciding of investor. The aim of the paper is monitoring operating costs with respect to initial costs of green buildings. The assessed environmentally friendly building are the new administrative building, the renovated administrative building and the administrative building built on the traditional method of construction. There is clearly presents differences in operating costs of monitored buildings in the paper. Operating costs are conversion to m3 of enclosed space and the number of people using facilities.. The article surveys the innovative approach of facility management into the development process of green buildings. The results presented are based on calculations and actually achieved values.