The Wisconsin Integrated Cropping Systems Trial has been comparing different farming systems on two farm sites in southern Wisconsin since 1989. Inexplicable differences in the yields of corn grown in three systems stimulated research on the relationship between yield and the dynamics of root growth. The three systems were continuous corn with mineral fertilizer (CS1), corn—soybean—winter wheat—red clover (CS3), and corn—oat + alfalfa—alfalfa with dairy manure applied (CS5). Four or five sequential root samplings were taken each growing season on two sites for 3 years. Soil monoliths were taken from around the base of the plant and washed out over a 1-mm sieve. Estimates were obtained of the length and health of roots from different nodes that were attached to the crown of the plant. The seasonal accumulation of root length was estimated by summing the maximal root length produced at each root node. Corn grown in monoculture averaged 7.5 Mg of grain/ha, which was similar to corn grown after red clover green manure (7.3 Mg/ha) but less than corn grown after alfalfa with manure (8.5 Mg/ha). Contrary to expectations, corn grown in monoculture averaged 26% more root length over the season than CS3 and 12% more length than CS5. The differences were mostly due to increased production of later sets of roots (nodes 6–9) for the corn in monoculture. However, for the first sets of nodes (seminal—node 5) the percentage of healthy roots was lower in the monoculture system (59%) than in CS3 (63%) or CS5 (76%). The increased root growth associated with corn grown in monoculture may be a response to poor root health. Regressions with root growth accounted for a large amount of the variation in grain yields. Corn grown after alfalfa with manure achieved higher yields with less roots than did corn grown in monoculture. Yields in the former system plateaued at root lengths of 1 cm/cm3 and greater, producing grain yields that ranged from 8 to 10 Mg/ha. Corn grown in CS1 and CS3 showed curvilinear responses with calculated yield maxima of 8.7 and 9.9 Mg/ha at root lengths of 2.12 and 1.74 cm/cm3, respectively. Intensifying the use of rotations and organic manures seemed to increase the ability of the corn rooting system to support grain yields. The cause for this greater efficiency is not yet clear, though root health may be an important factor.