The debate on land use policy is often turbid, due to a focus on policy means despite the absence of explicit policy objectives. To increase transparency of policy formulation, scientific tools can be used that make explicit possible trade-offs among policy objectives and uncertainties on effects of policy means. During the last decade, tools have been developed based on quantitative systems analysis (QSA) with the purpose of stimulating more fact-driven judgement of agricultural production systems that can contribute to rural development. These tools can be used in different phases of policy formulation to address different policy questions with various time and spatial scales. This paper describes a new QSA tool developed and applied in a case study in South Mali which addressed short-term effects of various policy instruments at farm level. The complementary role of this predictive QSA tool compared with tools that explore strategic land use options and consequences of conflicting aims is discussed. The potential of QSA tools in the policy formulation process is discussed and suggestions are made to enhance their impact.