The increased interest in Integrated Assessment (IA) of agricultural systems reflects the growing complexity of policy objectives and corresponding impacts related to this sector. The paper contemplates on the status of quantitative tools for IA in agriculture, drawing on recent European experiences from the development and application of large-scale integrated modelling systems which are both multi-dimensional/disciplinary and covering multiple spatial scales. Specific challenges arise from the numerous roles of agriculture with societal relevance, the heterogeneity of farms and farming systems across a geographical region and the multitude of environmental impacts of interest associated with agricultural production. Conceptual differences between typical bio-physical and economic models as well as deficiencies regarding validation and uncertainty analysis require continued efforts to improve the tools.