Sales of organic products reached $8 billion in the U.S. in 2000, continuing the nearly decade-long trend of 20% annual growth. In Iowa alone, organic production for all crops was 5265 ha (13,000 acres) in 1995 but 60,750 ha (150,000 acres) in 1999. Despite the growth in organic agriculture, our knowledge of organic farming systems remains limited. We have adopted a systems theory approach in our current research program at Iowa State University (ISU) to help address this gap in understanding. Systems theory holds that biological systems, such as agroecosystems, consist of integrated units of people, plants, animals, soil, insects and microorganisms, and each subsystem provides feedback to the other. In order to obtain input on research questions and experimental design, the Leopold Center for Sustainable Agriculture and ISU held six focus groups across Iowa in 1998 before long-term site establishment. Producers and agricultural professionals at the focus groups supported the need for long-term agroecological research (LTAR) sites in four distinct agroecological zones in Iowa. The goal of each LTAR is to examine the short- and long-term physical, biological, and socioeconomic effects of organic and conventional farming systems. By establishing long-term experiments, we are testing the hypothesis that longer crop rotations, typical of organic farms, provide yield stability, improve plant protection, and enhance soil health and economic benefits compared to conventional systems with shorter rotations and greater off-farm inputs. Examples of research results from two LTAR experiments in Iowa include similar pepper (Capsicum annuum) and soybean (Glycine max) yields in the conventional and organic systems. Organic systems used mechanical weed control and locally produced compost in place of synthetic fertilizers. Feedback from the local farm associations that are responsible for farm stewardship and farm finances is inherent in the LTAR process.