Responses of equine skeletal muscle characteristics to growth and training have been shown to differ between breeds. These differential responses may arise in part because muscle fiber type and mitochondrial density differ between breeds, even in untrained racing-bred horses. However, it is not known when these breed-specific differences manifest. To test the hypothesis that weanling Standardbreds (SB) and Thoroughbreds (TB) would have higher mitochondrial measures than Quarter Horses (QH), gluteus medius samples were collected from SB (mean SD; 6.2 1.0 mo; n = 10), TB (6.1 0.5 mo; n = 12), and QH (7.4 0.6 mo; n = 10). Citrate synthase (CS) and cytochrome c oxidase (CCO) activities were assessed as markers of mitochondrial density and function, respectively. Mitochondrial oxidative (P) and electron transport system (E) capacities were assessed by high-resolution respirometry (HRR). Data for CCO and HRR are expressed as integrated (per mg protein and per mg tissue wet weight, respectively) and intrinsic (per unit CS). Data were analyzed using PROC MIXED in SAS v 9.4 with breed as a fixed effect. Mitochondrial density (CS) was higher for SB and TB than QH (P 0.0007). Mitochondrial function (integrated and intrinsic CCO) was higher in TB and QH than SB (P 0.01). Integrated CCO was also higher in TB than QH (P < 0.0001). However, SB had higher integrated maximum P (PCI+II) and E (ECI+II) than QH (P 0.02) and greater integrated and intrinsic complex II-supported E (ECII) than both QH and TB (P 0.02), while TB exhibited higher integrated P with complex I substrates (PCI) than SB and QH (P 0.003) and higher integrated PCI+II and ECI+II than QH (P 0.02). In agreement, TB and QH had higher contribution of complex I (CI) to max E than SB (P 0.001), while SB had higher contribution of CII than QH and TB (P 0.002). Despite having higher mitochondrial density than QH and TB, SB showed lower CCO activity and differences in contribution of complexes to oxidative and electron transport system capacities. Breed differences in mitochondrial parameters are present early in life and should be considered when developing feeding, training, medication, and management practices.