Our objective was to compare the ranking of dairy cows according to their methane (CH) emissions as measured by a respiration chamber (RC) technique and the GreenFeed (GF) technique during 3 periods in second lactation. Two-day CH measurements in a RC performed in wk 3, 14, and 42 of lactation were flanked by GF measurements for 20 (period 1 [P1]), 35 (period 2 [P2]), and 35 (period 3 [P3]) days, respectively, before and after RC measurement. This gave the total duration of CH measurements using the GF system of 40, 70, and 70 d for P1, P2, and P3, respectively. Mean daily CH production (g/d) of the 8 dairy cows was 346, 439, and 430 using the RC technique and 338, 378, and 416 using the GF system during P1, P2, and P3, respectively. Average daily CH production determined by the GF technique was 2.4, 13.8, and 3.2% lower in P1, P2, and P3, respectively. Methane normalized to DMI continuously increased from P1 to P3 when measured in a RC, whereas it was lowest during P2 when measured by the GF method. Ranking of the cows according to CH production, CH/energy-corrected milk yield (ECM; CH/ECM), and CH/DMI differed between periods no matter which method was used. Cluster analysis including all 3 periods, however, identified the same cows with the highest and lowest CH production determined either by the RC technique or the GF system. In conclusion, multiple CH measurements at different stages of lactation are necessary for reliable discrimination of highest and lowest CH emitting cows and the GF system may be used to discriminate the extremes.