Selecting sites is an essential step in enabling the assessment of the impact of Integrated Agricultural Research for Development (IAR4D) in the Lake Kivu Pilot Learning Site. This paper reports on the process of identifying distinct administrative territories (sites) in which to establish innovation platforms and to monitor similar communities that are experiencing alternative agricultural research for development interventions. We show how the research design for the Sub- Saharan Africa Challenge Programme (SSACP) has been modified to take into account the key conditioning factors of the LKPLS without relinquishing robustness. A key change is the explicit incorporation of accessibility to multiple markets. Candidate sites were stratified according to the national political context, followed by good and poor accessibility to markets and finally according to security considerations and agro-ecology. Randomisation was carried out at all levels, although the need for paired counterfactual sites required the diagnosis of conditioning factors at the site level. Potential sites were characterised in terms of existing or recent agricultural research initiatives, as well as local factors that would have a direct effect on the success of interventions seeking to improve productivity, ameliorate the degradation of natural resources and enhance incomes through better links to markets. Fourteen sites were selected during the initial phase, and a further ten sites were added one year afterwards due to the need for more innovation platforms to test IAR4D. The site selection was successful in pairing action and counterfactual sites in terms of the baseline socioeconomic conditions of farming households. The unavoidable proximity of action and counterfactual sites, however, allows the possibility of spill-over effects and could reduce the measurable impact of IAR4D.