In this study we have compared GHG emissions from organic and conventional production systems, and also investigated how the conclusions about the emissions from different systems can be affected by the end uses of by-products of production (i.e., animal wastes and crop residues). These analyses have been conducted using the farm gate as a boundary (on-site emissions), and also including emissions beyond the farm gate to give a measure of the total impact of each production system [5], in order to demonstrate the significance of boundary selection in GHG emission assess- ments. Two baseline systems from the Nafferton Factorial Systems Comparison trial were compared with alternatives with varying end uses of agricultural by-products, which could dramatically alter the GHG balance for each of these systems. The on-site and total impacts were compared for baseline and alternative scenario