Nitrate leaching from crop rotations for organic grain production were investigated in a field experiment on different soil types in Denmark from 1997 to 2002. Three experimental factors were included in the experiment in a factorial design: 1) proportion of grass-clover and pulses in the rotation, 2) cover crop (with and without), and 3) manure (with and without). Two four-course rotations were compared. They had one year of grass-clover as a green manure crop, either followed by spring wheat or by winter wheat. The nitrate leaching was measured using ceramic suction cells. The nitrate leaching did not differ between the rotations, as a change in leaching following the grass-clover was compensated by a reverse effect in the grain crops. Use of cover crops reduced N leaching by 23 to 38% at crop rotation level with the highest reduction on the coarse sandy soil. Simulation of N leaching using the FASSET model showed that a practice of using part of the summer period in the grass-clover as a bare fallow to control couch grass could increase leaching substantially, in particular on the sandy soil