The objective was to study repeatability and sources of variation in feed conversion efficiency [FCE, milk kg/kg dry matter intake (DMI)] of lactating cows in mid to late lactation. Trials 1 and 2 used 16 cows (106 to 368d in milk) grouped in 8 pairs of 1 high- and 1 low-FCE cow less than 16d in milk apart. Trial 1 determined the repeatability of FCE during a 12-wk period. Trial 2 quantified the digestive and metabolic partitioning of energy and N with a 3-d total fecal and urine collection and measurement of CH4 and CO2 emission. Trial 3 studied selected ruminal methanogens in 2 pairs of cows fitted with rumen cannulas. Cows received a single diet including 28% corn silage, 27% alfalfa silage, 17% crude protein, and 28% neutral detergent fiber (dry matter basis). In trial 1, mean FCE remained repeatedly different and averaged 1.83 and 1.03 for high- and low-FCE cows, respectively. In trial 2, high-FCE cows consumed 21% more DMI, produced 98% more fat- and protein-corrected milk, excreted 42% less manure per kilogram of fat- and protein-corrected milk, but emitted the same daily amount of CH4 and CO2 compared with low-FCE cows. Percentage of gross energy intake lost in feces was higher (28.6 vs. 25.9%), but urinary (2.76 vs. 3.40%) and CH4 (5.23 vs. 6.99%) losses were lower in high- than low-FCE cows. Furthermore, high-FCE cows partitioned 15% more of gross energy intake toward net energy for maintenance, body gain, and lactation (37.5 vs. 32.6%) than low-FCE cows. Lower metabolic efficiency and greater heat loss in low-FCE cows might have been associated in part with greater energy demand for immune function related to subclinical mastitis, as somatic cell count was 3.8 fold greater in low- than high-FCE cows. As a percentage of N intake, high-FCE cows tended to have greater fecal N (32.4 vs. 30.3%) and had lower urinary N (32.2 vs. 41.7%) and greater milk N (30.3 vs. 19.1%) than low-FCE cows. In trial 3, Methanobrevibacter spp. strain AbM4 was less prevalent in ruminal content of high-FCE cows, which emitted less CH4 per unit of DMI and per unit of neutral detergent fiber digested than low-FCE cows. Thus lower digestive efficiency was more than compensated by greater metabolic efficiencies in high- compared with low-FCE cows. There was not a single factor, but rather a series of mechanisms involved in the observed differences in efficiency of energy utilization of the lactating cows in this study.