Improving the efficiency of livestock production is a promising way to reduce CH4 emissions from farming systems. The aims of this study were to: (1) assess effects of lactation number, genetic line and feeding system on estimated enteric and manure CH4 emissions from dairy cows prior to entering the milking herd and over a lactation period (i.e., whilst lactating and not lactating) per kg of energy corrected milk (ECM) (2) identify the main factors influencing a dairy cow's total lifetime CH4 emissions/kg ECM, and (3) suggest how animal and system effects could contribute to effective CH4 emission mitigations. This study utilized production data to predict enteric and manure CH4 emissions from the Langhill Holstein–Friesian dairy herd, which is part of a long term experiment to evaluate genetic line × feeding system interactions. Data were from January 1990 to 2002 at Farm 1 and 2003 to June 2008 at Farm 2. Total CH4 emissions (i.e., enteric and manure) were estimated for 824 cows, for a total of 1639 lactations. Cows were either on a low forage with grazing at Farm 1 or non-grazing at Farm 2, or high forage with grazing at both Farm 1 and 2, feeding system. Within each feeding system, cows belonged to genetic lines selected for increased milk fat plus crude protein (CP) yield (Select) or selected to remain close to the average genetic merit for milk fat plus CP yield (Control) for Holstein–Friesians evaluated in the UK annually. Total CH4 emissions from non-milking cows and manure CH4 emissions from lactating cows were predicted using Intergovernmental Panel on Climate Change Tier II methodology (1997), whilst enteric CH4 emissions for lactating cows were estimated using a non-linear equation (Mills et al., 2003) based on metabolizable energy intake. Residual Maximum Likelihood was used to assess effects of lactation number, genetic line, feeding system, as well as the main factors influencing dairy system CH4 emissions. Results show that cows maintained on the low forage feeding system produced ∼8% less enteric CH4 emissions/kg ECM versus the high forage system. At Farm 2, there was no difference in total CH4 emissions between a non-grazing low forage feeding system and a high forage system because lower enteric CH4 emissions were compensated for by higher manure CH4 emissions associated with slurry production. Cows selected for increased milk fat plus CP yield (Select) had lower total CH4 emissions/kg ECM up to their third lactation but, over a lifetime, there appears to be no meaningful reduction compared to Control cows. Higher dry matter intake and a longer lactation period, which were positively correlated with average ECM yield, were associated with lower total lifetime CH4 emissions/kg ECM.