There has been much interest in recent years in the potential for sequestering C in agricultural soils through changes in management. Unfortunately, scientific examination of this isue has historically been hampered by experimental difficulties, primarily the low signal to noise ratio of soil C measurements. Recent improvements in micrometeorological instrumentation now allow a different approach: near-continuous measurement of surface-atmosphere CO2 exchange. When supplemented with models to fill inevitable gaps in the measurement record, these data in principle allow estimation of C sequestration as the difference between the integrated flux and the C removed in the harvest. In practice, the uncertainties are sufficiently large that it may not always be possible to adequately resolve absolute C sequestration; we have found that the most powerful application is in paired-flux experiments, where measurements are made in adjacent fields with similar equuipment. These have allowed us to examine the relative impact of reduced tillage, and of the inclusion of cover crops in corn/soybean rotations.