Resilience, vulnerability and adaptability have emerged as dominant concepts in the study of disturbance and change of social-ecological systems. We analyze the conceptual, methodological and operational aspects in using these concepts for the assessment and analysis of agricultural systems and try to identify differences and possible overlaps between them. The analysis is performed considering a number of published studies on agricultural systems over a wide geographical range where these concepts have been applied. Our results show a clear conceptual overlap and often the exchangeable use of the concepts. Furthermore, the driving methodological and operational criteria for their application could not be separated unambiguously. It was, thus, difficult to identify guiding principles for the operational application of the individual concepts. We stress that the operationalization of these concepts requires consistency in the approaches and protocols to ensure their coherent use. We also argue that the conceptual and operational integration of resilience, vulnerability and adaptability would perhaps lead to a more complete portrayal of the behavior of agricultural systems in changing situations. But this requires more research including the development of operational protocols for which the premises of complexity, participation and functionality seem key.