The concentration of short branched-chain fatty acids, specifically 4-methyloctanoic acid (MOA) and 4-methylnonanoic acid (MNA), in subcutaneous fat were determined in five genotypes (Poll Dorset × Border Leicester Merino, Poll Dorset × Merino, Poll Dorset_muscling × Merino, Merino × Merino, Border Leicester × Merino) of Australian sheep. In total, 264 ewes and wethers, either 8 or 22 months of age, were selected for genotype, age and gender. These animals were sired by 16 rams that were selected for growth based on estimated breeding values (EBVs), except for one group (Poll Dorset_muscling × Merino), which was selected for muscling based on EBVs. There was a strong relationship between the concentration of MOA and MNA at 8 and 22 months of age. There were no differences between lambs sired by Poll Dorset rams selected for muscling or growth. The 8- and 22-month-old Poll Dorset × Merino sheep had higher levels of MOA and MNA compared with the other genotypes (P < 0.001). At 8 months of age, the wethers had higher levels of MOA and MNA (P < 0.001) than the ewes of the same genotype. There was a strong relationship (P < 0.001) between MOA and MNA and the fat and lean percentage for 22-month-old ewes. Effects of sire, dam and slaughter day (at the same slaughter age) on MOA and MNA were also found. The results suggest that there is good feasibility for selection against animals at risk of possessing higher levels of short branched-chain fatty acids.