This document outlines an objectives and methodology for analyzing complex agricultural problems and developing agricultural innovation strategies using the Rapid Appraisal of Agricultural Innovation Systems (RAAIS) tool. The document defines key characteristics of complex agricultural problems as multi-dimensional, multi-level, multi-stakeholder, and highly uncertain. It then describes the RAAIS workshop methodology which involves exercises to identify constraints, opportunities, and entry points for innovation through stakeholder participation. The goal is to facilitate analysis of problems and development of coherent strategies to address them through an agricultural innovation systems approach.