Body weight and adiposity are controlled by energy intake and energy expenditure. We have identified differences in hypothalamic set point for appetite regulating peptides in sheep selectively bred to be either lean or obese¹ . How this translates into the lean or obese phenotype in these animals is unknown as body weight and food intake are similar¹ . Here we aimed to measure post-prandial temperature in fat and muscle, to ascertain whether a difference in thermogenesis is the cause of the difference in body composition. Adult ewes (n=7 lean; n=8 obese) were studied. These had intracerebroventricular (icv) cannulae and temperature probes (Dataloggers) implanted into the retroperitoneal fat and the hind-limb skeletal muscle. Animals were meal fed (1100-1600h) to entrain post-prandial thermogenesis.  Food intake was monitored but there were no differences between lean and fat animals. Post-prandial thermogenesis was greater (P<0.05) in the retroperitoneal adipose tissue of lean animals (obese: 0.86±0.12 vs lean: 1.16±0.1 °C). Skeletal muscle temperature was similar in both groups. Icv infusion of leptin reduced (P<0.05) food intake equally in lean and obese animals. Post-prandial expression of UCP1 mRNA was greater (P<0.05) in retroperitoneal fat of lean animals than in obese animals, but UCP3 expression in skeletal muscle was similar in the two groups. Mitochondrial genome sequencing showed that lean and obese animals displayed distinct haplotypic clustering of mitochondrial DNA within both the encoding and non-encoding (D-loop) regions. This demonstrates that differences in body composition are underpinned by differences in thermogenesis, specifically within adipose tissue. Furthermore, thermogenic differences are associated with specific mitochondrial DNA haplotypes suggesting a strong genetic component inherited through the maternal lineage.