Capacity development interventions in support of agricultural innovation are more effective when based on systematic and participatory assessments of existing skills and capacity needs. Recognizing that, an instrument has been developed in the context of the Capacity Development for Agricultural Innovation Systems (CDAIS) project. It consists of a capacity scoring tool that allows assessing innovation capacities, identifying strengths and weaknesses and monitoring capacity changes over time. This paper describes the scoring tool and provides guidelines on how to apply it successfully.