Under the Kyoto protocol of the United Nations Framework Convention on Climate Change the United States is charged with reducing emissions of greenhouse gases to seven percent below their 1990 levels by the period 2008-2012. These reductions could be met from many industries including agriculture. In this paper, an economic simulation model is linked to an ecosystem model to quantify the economic efficiency of policies that might be used to sequester carbon (C) in agricultural soils in the Northern Plains region. Simulations with the Century ecosystem model show that long-term soil C levels associated with a crop/fallow system are less than those for grass alone, but that soil C levels for grass-clover-pasture are greater than for continuously cropped grains. The analysis shows that a CRP-style policy is found to be an inefficient means to increase soil C because the per acre payments to convert crop-land to grass-only draw land from both the crop/fallow system and the continuous cropping system, and costs typically exceed $100 per MT (metric ton) of C. In contrast, payments to adopt continuous cropping were found to produce increases in soil C for between $5 to $70 depending on area and degree of targeting of the payments. The most efficient, lowest cost policy is achieved when payments are targeted to land that was previously in a crop/fallow rotation. In this range, soil C sequestration appears to be competitive with C sequestered from other sources.