Farmers are the primary managers and designers of their agroecosystems. As the ultimate integrators of technologies within the biological, social and economic complexity of agroecosystems, their role as decision makers is increasingly respected.  The farmers’ role as a participant in agroecosystems research and design is evolving.  These roles range from facilitating formal hypotheses testing by graduate students to being the subjects of case studies to influencing research design and setting the research agenda. In southern New England, five farmer research groups were developed to systematically investigate farmers’ own ideas. A key objective was to engage small groups of farmers in solving their own problems in the context of their own systems. The five groups were initiated and evolved differently.  The groups had different qualities of scientific outcomes and led to different kinds of change in local farming systems. They resulted in different levels of influence on the scientific agenda. Facilitating the different groups provided unique challenges to project leaders and scientists.  Negotiation and flexibility were required to assure statistically useful or at least original information was generated by each project.  A farmer-led,  on-farm research approach has strengths and limitations, but is an excellent, sometimes critical starting point for field research.