This study investigated the relationships between methane (CH4) emission and fatty acids, volatile metabolites (V) and non-volatile metabolites (NV) in milk of dairy cows. Data from an experiment with 32 multiparous dairy cows and four diets were used. All diets had a roughage : concentrate ratio of 80 : 20 based on dry matter (DM). Roughage consisted of either 1000 g/kg DM grass silage (GS), 1000 g/kg DM maize silage (MS), or a mixture of both silages (667 g/kg DM GS and 333 g/kg DM MS; 333 g/kg DM GS and 677 g/kg DM MS). Methane emission was measured in climate respiration chambers and expressed as production (g/day), yield (g/kg dry matter intake; DMI) and intensity (g/kg fat- and protein-corrected milk; FPCM). Milk was sampled during the same days and analysed for fatty acids by gas chromatography, for V by gas chromatography–mass spectrometry, and for NV by nuclear magnetic resonance. Several models were obtained using a stepwise selection of (1) milk fatty acids (MFA), V or NV alone, and (2) the combination of MFA, V and NV, based on the minimum Akaike’s information criterion statistic. Dry matter intake was 16.8±1.23 kg/day, FPCM yield was 25.0±3.14 kg/day, CH4 production was 406±37.0 g/day, CH4 yield was 24.1±1.87 g/kg DMI and CH4 intensity was 16.4±1.91 g/kg FPCM. The observed CH4 emissions were compared with the CH4 emissions predicted by the obtained models, based on concordance correlation coefficient (CCC) analysis. The best models with MFA alone predicted CH4 production, yield and intensity with a CCC of 0.80, 0.71 and 0.69, respectively. The best models combining the three types of metabolites included MFA and NV for CH4 production and CH4 yield, whereas for CH4 intensity MFA, NV and V were all included. These models predicted CH4 production, yield and intensity better with a higher CCC of 0.92, 0.78 and 0.93, respectively, and with increased accuracy (Cb) and precision (r). The results indicate that MFA alone have moderate to good potential to estimate CH4 emission, and furthermore that including V (CH4 intensity only) and NV increases the CH4 emission prediction potential. This holds particularly for the prediction model for CH4 intensity.