The northern mountain region of Vietnam (NMR) is dominated by swidden/fallow farming systems. The fallow land of these systems is populated by small trees and bushes. Since the 1960s the government of Vietnam has tried to limit or stop swiddening and replace it with permanent upland agricultural fields, paddy, fruit trees and animal husbandry. Discussion in the policy debate and literature focuses on the impacts these changes have on local people's livelihoods. There have been no attempts to evaluate the impact of these changes on greenhouse gas (GHG) emissions. This paper examines the realities of current farming system changes taking place at the hamlet level and other changes that could take place due to government land use policies and extension programs. The paper answers the following questions: How could farming system changes influence net GHGs? Which farming system changes in the NMR, the trajectories of changes that are currently observed or those that would be followed if farmers adhere strictly to government policies and programs, will have a greater affect on the GHG contributions from agriculture in the region? Could ‘clean development mechanism' (CDM) projects make a difference in the profitability of the pathways mentioned? Results show: (1) if farming systems in the NMR continue along currently observed change trajectories there will be increases in GHG emissions; (2) if the NMR farming systems change according to government policies and programs there will be a net sequestration of carbon in regrowing vegetation during the initial 20 years; (3) over the longer term, in areas where systems change to fit government policies, increased GHG emissions from other changes in the farming systems (e.g. increased paddy and increased pig raising in sties) will overtake the amounts of carbon sequestered in vegetation; (4) CMD projects only make a difference if (a) maximum biomass potential of regrowing fallow can be reached; (b) a favourable baseline is chosen; (c) timing and length of the accounting period is correct; and (d) farmers do not take compensatory action in response to government policies. Given these conditions it does not appear that currently envisioned clean development mechanisms would be beneficial to farmers in the NMR.