Based on the interest of organic and conventional farmers in Iowa in long-term analysis of organic systems, the Neely-Kinyon Long-Term Agroecological Research (LTAR) site was established in 1998 to examine the agronomic and economic performance of conventional and organic systems, using certified organic production practices. We report the results of the economic analysis from 3 years of production (1999–2001). Using organic price premiums for organic crops, returns for corn within the organic corn-soybean-oat and corn-soybean-oat-alfalfa rotations were significantly greater than conventional corn-soybean rotation returns (US$126 ha−1). Com returns were not significantly different between the two organic rotations, at US$655 ha−1 and US$674 ha−1, respectively. Returns for soybean within the organic corn-soybean-oat and com-soybean-oat-alfalfa rotations were not significantly different, at US$1233 ha−1 and US$1326 ha−1, respectively. Organic soybean returns were significantly greater than conventional soybean crop returns (US$235 ha−1) in the corn-soybean rotation. Rotational 3-year average returns were US$180 ha−1 for the conventional corn-soybean rotation, compared to US$734 ha−1 for the organic corn-soybean-oat and US$739 ha−1 for the organic com-soybean-oat-alfalfa rotation.