Associations between animal behaviour and emissions of methane (CH4) and ammonia (NH3) have been noted in studies of grazing cattle (Lockyer, 1997) and feedlot confined cattle (Harper et al., 1999, Flesch et al., 2007). Methane emissions have been predicted as being greatest during bouts of rumination (Harper et al., 1999) whereas the emissions of the indirect greenhouse gas ammonia tends to be low early in the morning but increasing rapidly in the early afternoon after which a rapid decline until sunset (Flesch et al., 2007). With the exception of Harper et al., (1999) there are few complete data sets that examine the interaction between animal behaviour and greenhouse gas emissions from intensive animal production systems. The current study aimed to investigate the relationship between animal behaviour and emissions of CH4 and NH3 in a beef feedlot system in northern Australia.