The development of sustainable cropping systems is a key priority for agronomists and crop scientists. A first step involves understanding the relationship between cropping system performance and farmers’ practices. To complete this step, a methodological framework entitled Regional Agronomic Diagnosis (RAD) has been developed. During the last ten years, the scope of the regional agronomic diagnosis has been enlarged to include several factors describing crop quality and the environmental impact of cropping systems. Regional agronomic diagnosis has led to several major advances such as (1) the assessment of the effect of preceding crop and soil structure on malting barley quality in France and (2) the assessment of the effects of ploughing, nematicide use and fertilisers on soil properties in intensive banana plantations in the West Indies. Improvements have also been gained in methodology, particularly by the selection of indicators for assessing the effects of crop management, soil and weather conditions, and data analysis. Finally, regional agronomic diagnosis has been integrated into more general approaches of agricultural development. We review here this methodological progress.