Agricultural innovation systems are complex, multi-layered, and can be difficult to define and analyse. In this paper, we provide examples of ‘systems analysis’: describing the context, what was done, and how the outcomes informed broader research and development activities. The five cases describe analyses of: i) agricultural systems in North-West Vietnam; ii) household food security in Central Vietnam; iii) agricultural innovation systems in Central Africa; iv) wheat commodity systems in Sub-Saharan Africa, and v) the national agricultural research system in Papua New Guinea.