The purpose of this paper is to describe the methodology developed in the first phase of the project, for an empirical study of the economic relationship between seed systems, access to crop genetic resources and farm level outcomes. The initial methodology was developed prior to conducting field work in the Hararghe region of Ethiopia based on the previous experience of the project team, reviews of the literature and discussions with experts in the area of seed systems and crop genetic diversity at FAO and the International Plant Genetic Resource Institute (IPGRI). The methodology was then updated based on visits to the field and in the design of the initial household survey. The methodology discussed in this document refers to the final approach taken, highlighting what was intended and what actually happened in the field. As part of this discussion, lessons learned are also noted. The intended audience for this publication includes researchers, technicians and specialists working in the field of agricultural biodiversity, seed systems and agricultural development. The hope is that by documenting the methodology and lessons learned this will provide assistance to those wishing to conduct similar research in this area.