Abstract. The northern Australian grains industry relies on nitrogen (N) fertiliser to optimise yield and protein, but N fertiliser can increase soil fluxes of nitrous oxide (N 2 O) and methane (CH 4 ). We measured soil N 2 O and CH 4 fluxes associated with wheat (Triticum aestivum) and barley (Hordeum vulgare) using automated (Expts 1, 3) and manual chambers (Expts 2, 4, 5). Experiments were conducted on subtropical Vertosol soils fertilised with N rates of 0-160 kg N ha -1 .In Expt 1 (2010), intense rainfall for a month before and after sowing elevated N 2 O emissions from N-fertilised (80 kg N ha -1 ) wheat, with 417 g N 2 O-N ha -1 emitted compared with 80 g N 2 O-N ha -1 for non-fertilised wheat. Once crop N uptake reduced soil mineral N, there was no further treatment difference in N 2 O. Expt 2 (2010) showed similar results, however, the reduced sampling frequency using manual chambers gave a lower cumulative N 2 O. By contrast, very low rainfall before and for several months after sowing Expt 3 (2011) resulted in no difference in N 2 O emissions between N-fertilised and non-fertilised barley. N 2 O emission factors were 0.42, 0.20 and -0.02 for Expts 1, 2 and 3, respectively. In Expts 4 and 5 (2011), N 2 O emissions increased with increasing rate of N fertiliser. Emissions were reduced by 45% when the N fertiliser was applied in a 50 : 50 split between sowing and mid-tillering, or by 70% when urea was applied with the nitrification inhibitor 3,4-dimethylpyrazole-phosphate.Methane fluxes were typically small and mostly negative in all experiments, especially in dry soils. Cumulative CH 4 uptake ranged from 242 to 435 g CH 4 -C ha -1 year -1 , with no effect of N fertiliser treatment. Considered in terms of CO 2 equivalents, soil CH 4 uptake offset 8-56% of soil N 2 O emissions, with larger offsets occurring in non-N-fertilised soils.The first few months from N fertiliser application to the period of rapid crop N uptake pose the main risk for N 2 O losses from rainfed cereal cropping on subtropical Vertosols, but the realisation of this risk is dependent on rainfall. Strategies that reduce the soil mineral N pool during this time can reduce the risk of N 2 O loss.