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In the Netherlands bookkeeping of inputs and outputs at the level of individual farms has been selected as a new solution to control nutrient use and to tax nutrient surpluses in agriculture. At the same time, nutrient accounting presents important management information. This paper presents a theoretical and historical background of the system, a description of the system as such and some first practical experiences. The relationship of the nutrient accounting system with the obligatory financial accounting is discussed and evaluated as crucial. The establishment of conformity of financial and nutrient accounts is an important audit instrument of the nutrient system as a policy instrument. Introduction in practice as a policy instrument will be phased.