Climatic conditions and cultural practices in the sub-tropical and tropical high-rainfall regions in which sugarcane is grown in Australia are conducive to rapid carbon and nitrogen cycling. Previous research has identified substantial exchanges of methane (CH4) and nitrous oxide (N2O) between sugarcane soils and the atmosphere. However, that research has been mostly short-term. This paper describes recent work aimed at quantifying exchanges of CH4 and N2O from fertilised sugarcane soils over whole growing seasons. Micrometeorological and chamber techniques provided continuous measurements of gas emissions in whole-of-season studies in a burnt-cane crop on an acid sulfate soil (ASS) that was fertilised with 160 kg nitrogen (N) ha-1 as urea in the south of the sugarcane belt (Site 1), and in a crop on a more representative trash-blanketed soil fertilised with 150 kg urea-N ha-1 in the north (Site 2). Site 1 was a strong source of CH4 with a seasonal emission (over 342 days) of 19.9 kg CH4 ha-1. That rate corresponds to 0.5-5% of those expected from rice and wetlands. The many drains in the region appear to be the main source. The net annual emission of CH4 at Site 2 over 292 days was essentially zero, which contradicts predictions that trash-blankets on the soil are net CH4 sinks. Emissions of N2O from the ASS at Site 1 were extraordinarily large and prolonged, totalling 72.1 kg N2O ha-1 (45.9 kg N ha-1) and persisting at substantial rates for 5 months. The high porosity and frequent wetting with consequent high water filled pore space and the high carbon content of the soil appear to be important drivers of N2O production. At Site 2, emissions were much smaller, totalling 7.4 kg N2O ha-1 (4.7 kg N ha-1), most of which was emitted in less than 3 months. The emission factors for N2O (the proportion of fertiliser nitrogen emitted as N2O-N) were 21% at Site 1 and 2.8% at Site 2. Both factors exceed the default national inventory value of 1.25%. Calculations suggest that annual N2O production from Australian sugarcane soils is around 3.8 kt N2O, which is about one-half a previous estimate based on short-term measurements, and although ASS constitute only about 4% of Australia's sugarcane soils, they could contribute about 25% of soil emissions of N2O from sugarcane. The uptake of 50-94 t CO2 ha-1 from the atmosphere by the crops at both sites was offset by emissions of CH4 and N2O to the atmosphere amounting to 22 t CO2-e ha-1 at Site 1 and 2 t CO2-e ha-1 at Site 2. © 2009 Elsevier B.V. All rights reserved.