Rice production worldwide represents a major anthropogenic source of greenhouse gas emissions. Nitrogen fertilization and irrigation practices have been fundamental to achieve optimal rice yields, but these agricultural practices together with by-products from plants and microorganisms, facilitate the production, accumulation and venting of vast amounts of CO2, CH4 and N2O. We propose that the development of elite rice varieties should target root traits enabling an effective internal O2 diffusion, via enlarged aerenchyma channels. Moreover, gas tight barriers impeding radial O2 loss in basal parts of the roots will increase O2 diffusion to the root apex where molecular O2 diffuses into the rhizosphere. These developments result in plants with roots penetrating deeper into the flooded anoxic soils, producing higher volumes of oxic conditions in the interface between roots and rhizosphere. Molecular O2 in these zones promotes CH4 oxidation into CO2 by methanotrophs and nitrification (conversion of NH4+ into NO3-), reducing greenhouse gas production and at the same time improving plant nutrition. Moreover, roots with tight barriers to radial O2 loss will have restricted diffusional entry of CH4 produced in the anoxic parts of the rhizosphere and therefore plant-mediated diffusion will be reduced. In this review, we describe how the exploitation of these key root traits in rice can potentially reduce greenhouse gas emissions from paddy fields.